the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
| 28 Jun 2022
FABM-NflexPD 2.0: Testing an Instantaneous Acclimation Approach for Modelling the Implications of Phytoplankton Eco-physiology for the Carbon and Nutrient cycles
Abstract. The acclimative response of phytoplankton, which adjusts their nutrient and pigment content in response to changes in ambient light, nutrient levels, and temperature, is an important determinant of observed chlorophyll distributions and biogeochemistry. Acclimative models typically capture this response and its impact on the C : nutrient : Chl ratios of phytoplankton by explicitly resolving the dynamics of these constituents of phytoplankton biomass. The Instantaneous Acclimation (IA) approach only requires resolving the dynamics of a single tracer and calculates the elemental composition assuming instantaneous local equilibrium. IA can capture the acclimative response without substantial loss of accuracy in both 0D box models and spatially explicit 1D models. A major draw-back of IA so far has been its inability to maintain mass balance for the elements with unresolved dynamics. Here we extend the IA model to capture both C and N cycles in a 0D setup, which requires analytical derivation of additional flux terms to account for the temporal changes in cellular N quota, Q. We present extensive tests of this model, with regard to the conservation of total C an N, and its behavior in comparison to an otherwise equivalent, fully explicit Dynamic Acclimation (DA) variant, under idealized conditions with variable light and temperature. We also demonstrate a modular implementation of this model in the Framework for Aquatic Biogeochemical Modelling (FABM), which facilitates modelling competition between an arbitrary number of different acclimative phytoplankton types. In a 0D setup, we did not find evidence for computational advantages of the IA approch over the DA variant. In a spatially explicit setup, performance gains may be possible, but would require modifying the physical-flux calculations to account for spatial differences in Q between model grid cells.
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Notice on discussion status
The requested preprint has a corresponding peer-reviewed final revised paper. You are encouraged to refer to the final revised version.
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Preprint
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The requested preprint has a corresponding peer-reviewed final revised paper. You are encouraged to refer to the final revised version.
- Preprint
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- Final revised paper
Journal article(s) based on this preprint
instantaneous acclimationapproach, in which the elemental composition of the phytoplankton is assumed to adjust to an optimal value instantaneously. Through rigorous tests, we evaluate the consistency of this scheme.
Interactive discussion
Status: closed
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RC1: 'Comment on egusphere-2022-493', Hoa Nguyen, 12 Aug 2022
The paper presented a model of phytoplankton instantaneous acclimation (IA), FABM-NflexPD 2.0 (K21), which was further developed from its earlier version FABM-NflexPD 1.0 (K11). The K21 was extended from K11 to account for and conserve both C and N fluxes. The K21 was said might lower in computational costs compared to its DA (Dynamic Acclimation) variant due to less state variables. The K21 was then tested in 4 scenarios and its performance was compared to its DA variant
The paper has achieved its goals, e.g., the model was successfully built and its performance was almost as same as the DA’s. However, the treatment of N mass balance (section 4.1) that made it violate the model assumption sounded unconvinced. Has the paper tried out alternative treatments to this issue? Might the paper state strength, weakness and applications of the K21?
Technical errors: (1) line 14: approach; (2) p.11, title of 3.3: "in simulating" appeared twice.
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Citation: https://doi.org/10.5194/egusphere-2022-493-RC1 -
RC2: 'Comment on egusphere-2022-493', Anonymous Referee #2, 18 Aug 2022
Kerimoglu and colleagues developed an updated version of their previously published plankton model FABM-NflexPD. In this version, they track both N and C biomass of phytoplankton assuming instantaneous acclimation (IA version of the model). In comparison to its previous version, this new version conserves both carbon and nitrogen in the system. Mass balance is ensured by analytically computing the temporal change in cellular N quota. In 0-D and pseudo 0-D setups, mass conservation is excellent and the model performs very well compared to a fully explicit treatment of the N quota (DA version of the model). However, the IA setup is not cheaper in terms of computing cost.Â
The paper is very well written, very clear and complete. I don't have any major issues on what is presented in the study. However, I should admit that I have trouble finding this paper interesting and useful. The main objective of this study, as stated by the authors, is to develop a model that mimics the behavior of a full quota model but that is cheaper so that it can be embedded in a global biogeochemical model. As a global biogeochemical modeller, I agree that it is a crucial point. And having less tracers in a global 3-D model is generally a good strategy to reduce the computing cost as transport of a tracer is very expensive. In the case of this study, I think that this main objective is not reached. First, the study is restricted to a pseudo 0-D (closed and opened) framework where transport with neighboring cells is not relevant and computing not an issue. Second, they claim that transposing this framework to a 1-D setup failed because mass is no more conserved. Obviously, spatial transport of a variable quota leads to the same problem as temporal evolution of this quota. As said in the manuscript, conserving mass in a 1-D or 3-D configuration would require to track the evolution of the quota due to transport to compute the additional fluxes of nutrients. To me, this is equivalent to explicitly transport the quota. Furthermore, it would require additional fluxes of nutrient that could possibly, especially when transport and spatial gradients are strong, significantly alter the model behavior. In other words, the computing cost would be identical for a result that may differ from the fully explicit model.Â
I have additional small questions. In T1, mass is not fully conserved in both model versions. Could the authors be more specific on why this is the case? In DA, is it simply truncation errors in single precision? In T2, differences in total N seem to be 0? Obviously, this is not exactly 0 because it is not the case in T1. Is the difference larger than in T1? In other words, I suggest to change the y-axis in a way similar to what is done in T1. Finally, in T3, the authors only show two figures. From these figures, it is difficult to see if the temporal evolution of the total phytoplankton biomass is changed and by how much.
To conclude, I find that the authors did not make the demonstration that the framework they developed in the study provides an interesting, cheaper alternative to model flexible nutrient quota in spatially explicit biogeochemical models. To be convinced, I think that including a 1-D experiment is necessary. This would also present how additional fluxes due to transport can be represented and if that framework is really cheaper than a full model. Without such an experiment, I think that this manuscript should be rejected.Â
Citation: https://doi.org/10.5194/egusphere-2022-493-RC2 - AC1: 'Response to Reviewers', Onur Kerimoglu, 15 Sep 2022
Interactive discussion
Status: closed
-
RC1: 'Comment on egusphere-2022-493', Hoa Nguyen, 12 Aug 2022
The paper presented a model of phytoplankton instantaneous acclimation (IA), FABM-NflexPD 2.0 (K21), which was further developed from its earlier version FABM-NflexPD 1.0 (K11). The K21 was extended from K11 to account for and conserve both C and N fluxes. The K21 was said might lower in computational costs compared to its DA (Dynamic Acclimation) variant due to less state variables. The K21 was then tested in 4 scenarios and its performance was compared to its DA variant
The paper has achieved its goals, e.g., the model was successfully built and its performance was almost as same as the DA’s. However, the treatment of N mass balance (section 4.1) that made it violate the model assumption sounded unconvinced. Has the paper tried out alternative treatments to this issue? Might the paper state strength, weakness and applications of the K21?
Technical errors: (1) line 14: approach; (2) p.11, title of 3.3: "in simulating" appeared twice.
Â
Citation: https://doi.org/10.5194/egusphere-2022-493-RC1 -
RC2: 'Comment on egusphere-2022-493', Anonymous Referee #2, 18 Aug 2022
Kerimoglu and colleagues developed an updated version of their previously published plankton model FABM-NflexPD. In this version, they track both N and C biomass of phytoplankton assuming instantaneous acclimation (IA version of the model). In comparison to its previous version, this new version conserves both carbon and nitrogen in the system. Mass balance is ensured by analytically computing the temporal change in cellular N quota. In 0-D and pseudo 0-D setups, mass conservation is excellent and the model performs very well compared to a fully explicit treatment of the N quota (DA version of the model). However, the IA setup is not cheaper in terms of computing cost.Â
The paper is very well written, very clear and complete. I don't have any major issues on what is presented in the study. However, I should admit that I have trouble finding this paper interesting and useful. The main objective of this study, as stated by the authors, is to develop a model that mimics the behavior of a full quota model but that is cheaper so that it can be embedded in a global biogeochemical model. As a global biogeochemical modeller, I agree that it is a crucial point. And having less tracers in a global 3-D model is generally a good strategy to reduce the computing cost as transport of a tracer is very expensive. In the case of this study, I think that this main objective is not reached. First, the study is restricted to a pseudo 0-D (closed and opened) framework where transport with neighboring cells is not relevant and computing not an issue. Second, they claim that transposing this framework to a 1-D setup failed because mass is no more conserved. Obviously, spatial transport of a variable quota leads to the same problem as temporal evolution of this quota. As said in the manuscript, conserving mass in a 1-D or 3-D configuration would require to track the evolution of the quota due to transport to compute the additional fluxes of nutrients. To me, this is equivalent to explicitly transport the quota. Furthermore, it would require additional fluxes of nutrient that could possibly, especially when transport and spatial gradients are strong, significantly alter the model behavior. In other words, the computing cost would be identical for a result that may differ from the fully explicit model.Â
I have additional small questions. In T1, mass is not fully conserved in both model versions. Could the authors be more specific on why this is the case? In DA, is it simply truncation errors in single precision? In T2, differences in total N seem to be 0? Obviously, this is not exactly 0 because it is not the case in T1. Is the difference larger than in T1? In other words, I suggest to change the y-axis in a way similar to what is done in T1. Finally, in T3, the authors only show two figures. From these figures, it is difficult to see if the temporal evolution of the total phytoplankton biomass is changed and by how much.
To conclude, I find that the authors did not make the demonstration that the framework they developed in the study provides an interesting, cheaper alternative to model flexible nutrient quota in spatially explicit biogeochemical models. To be convinced, I think that including a 1-D experiment is necessary. This would also present how additional fluxes due to transport can be represented and if that framework is really cheaper than a full model. Without such an experiment, I think that this manuscript should be rejected.Â
Citation: https://doi.org/10.5194/egusphere-2022-493-RC2 - AC1: 'Response to Reviewers', Onur Kerimoglu, 15 Sep 2022
Peer review completion
Journal article(s) based on this preprint
instantaneous acclimationapproach, in which the elemental composition of the phytoplankton is assumed to adjust to an optimal value instantaneously. Through rigorous tests, we evaluate the consistency of this scheme.
Model code and software
OnurKerimoglu/fabm-nflexpd: FABM-NflexPD Version 2.0 release candidate 0 Onur Kerimoglu https://doi.org/10.5281/zenodo.6600755
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Markus Pahlow
Prima Anugerahanti
Sherwood Lan Smith
The requested preprint has a corresponding peer-reviewed final revised paper. You are encouraged to refer to the final revised version.
- Preprint
(769 KB) - Metadata XML