the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
A new global dataset of photosynthesis parameters
Abstract. Photosynthesis-irradiance and photosynthesis-depth experiments are two standard ways of experimentally quantifying primary production. These measurements have historically formed the backbone for the formulation of mathematical models of primary production and to this day remain an invaluable resource for model development and refinement. From such experiments information on photosynthesis parameters can be extracted, which allows for the quantification of the photosynthesis light dependence, essential in the calculation of primary production. To this day, this is the only avenue for photosynthesis parameters estimation, making such data invaluable for primary production modelling. In the literature, there have been several efforts to form global datasets of photosynthesis parameters, collected at various sites across the world oceans and seas. Here, we use a publicly available global dataset of in situ primary production profiles and construct a new database of photosynthesis parameters. We use an inverse modelling approach that is described in great details, along with the data requirements. For a forward model, we employ a fully solvable analytical model of the production profile, and we use the inverse model to compare it with the measured production profile, while constraining it with measured daily watercolumn production. Using this approach, we successfully recovered 4160 photosynthesis-irradiance parameters from the global oceans, which enabled a model versus data comparison for watercolumn production. The spatio-temporal distribution of the new dataset is presented and compared to existing datasets. Finally, the new photosynthesis parameters dataset is provided publicly, along with metadata needed for the implementation in primary production models.
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Status: final response (author comments only)
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RC1: 'Comment on essd-2025-820', Valeria Segura, 26 May 2026
The comment was uploaded in the form of a supplement: https://essd.copernicus.org/preprints/essd-2025-820/essd-2025-820-RC1-supplement.pdfCitation: https://doi.org/
10.5194/essd-2025-820-RC1 - CC1: 'Reply on RC1', Zarko Kovac, 12 Jun 2026
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RC2: 'Comment on essd-2025-820', Anonymous Referee #2, 07 Aug 2026
Photosynthesis parameters play crucial roles in remote estimation of phytoplankton primary production. This study presents a new global dataset of photosynthesis parameters that derived from the in situ primary production profiles compiled by Mattei and Scardi (2021). The work addresses an important limitation in marine primary production modelling by improving the availability of photosynthesis parameters, which are difficult to obtain from remote sensing and remain sparsely sampled across the global oceans. The proposed inverse modelling framework is appropriate for the study and makes effective use of a large global observational archive by combining the shape of the normalized production profile with water column production. Overall, the manuscript is well organized, and the objectives, methods, results, and discussion are presented clearly. However, the following issues need to be further addressed before the manuscript is suitable for publication.
Abstract
Line 16 reports that 4160 photosynthesis irradiance parameters were recovered, whereas Lines 375-376 state that 3776 parameter pairs were obtained. These two numbers are confusing and should be explained more clearly. Please clarify what each number represents and use consistent terminology throughout the manuscript.
Introduction
Line 32 “Global scale chlorophyll concentration …” — should this be revised to “chlorophyll-a concentration”? Please check and apply this correction consistently throughout the manuscript.
Lines 34-36 The statement that direct measurements are the only way to estimate photosynthesis parameters may be misleading. Since this study estimates these parameters using an inverse modelling approach, it would be clearer to distinguish between directly measured parameters and model derived estimates.
Lines 85-90, the authors mentioned the global database and codes for data access are made freely available. However, the Data Availability section appears to provide only the dataset location. The authors need to provide a dedicated Code Availability section describing the availability of the preprocessing, forward model, inverse optimization, and quality control code. If some parts cannot be made publicly available, this should be stated clearly.
Inverse model
The terminology must be used consistently throughout the manuscript. For example, "watercolumn", "water column", and "water-column" should be standardized. It would also be helpful to include a table summarizing all symbols, their definitions, units, and whether they are measured or estimated.
Lines 105-110 use the light formulation of Platt et al. (1990) and Kovač et al. (2016a). Although this approach has been verified previously, the authors need to clarify why the approach is applicable for generating this global dataset of this study, particularly for profiles with reconstructed PAR and a single attenuation coefficient.
Lines 120-121, it is recommended that the authors integrate the Appendix A and Appendix B into the main text, as the inversion algorithm is one of the most crucial factors for determining the quality of the results in this study.
Equation (10) combines the residuals at individual depths with one residual for normalized water column production. However, the manuscript does not explain whether these two terms are weighted or scaled before they are combined. Since they may differ in magnitude, their relative influence on the optimization should be clarified. Lines 337-343 state that the water column constraint improves convergence, but the authors should also explain how this term affects the estimated parameters.
Production profiles dataset
Lines 197-200 report 6084 profiles, including 5578 from the Northern Hemisphere and 478 from the Southern Hemisphere. Mattei and Scardi (2021) additionally classify 28 profiles as Equator, which completes the total of 6084. Please include this category explicitly. In addition, the manuscript reports 37722 observations in Line 198 but 37723 in Line 321. These numbers should also be verified and kept consistent throughout the manuscript.
Lines 201-209, some of the input data were filled using satellite products or interpolation rather than direct measurements. Since these data are used to estimate the photosynthesis parameters, it would be helpful to discuss how they may affect the final results. The authors are encouraged to compare the estimated parameters obtained from fully measured profiles with those containing gap filled data. In addition, including the data source and gap filling information for each published record would improve the usefulness of the dataset.
Lines 246-254, the requirement of at least five measurement depths needs further justification. According to the manuscript, six depths are considered sufficient, while five depths represent the minimum requirement, but no quantitative evidence is provided to support this conclusion. I encourage the authors to include a simple sensitivity analysis showing how the estimated parameters change with different numbers of measurement depths.
Results
The Figure 5 caption states that the vertical axis represents the percentage of profiles, whereas the figure appears to show the number of profiles. The authors need to correct either the caption or the axis labels.
Lines 315-343 describe the results as model accuracy. However, the same production profiles and normalized water column production values are used to estimate the parameters, and water column production is also included in Equation (10). Therefore, Figure 6 represents goodness of fit or internal reconstruction performance rather than independent validation. The authors should conduct cross validations to verify the performances of the inverse model.
The reported R2 (=71.31%) (Line 336) is insufficient to characterize model performance. The authors need to report RMSE, MAE, bias, and sample size for both production at depth and water column production, as well.
The caption of Figure 6 should state the number of profiles included and the screening or quality flag criteria applied before plotting. In addition, given the substantial overlap among points, a density-based representation may be more informative than a conventional scatter plot.
Discussion
The manuscript discusses the differences between parameters derived from approximately 24-hour in situ incubations and those obtained from shorter controlled light experiments. ( Lines 367-381, 441-453) These differences should also be reflected in the discussion of dataset complementarity and potential applications. It should be made clear that the two datasets are not directly comparable without considering the differences in the experimental methods.
Lines 41-413, For your information, a previous study published on the journal of Remote Sensing of Environment (https://doi.org/10.1016/j.rse.2022.113027) has proposed a machine learning-based method to remotely estimate photosynthesis parameters.
Conclusions
Lines 455-462, the Conclusions overstate the strength of the model evaluation. The model performance is described as "quite good" based on an of 0.7131, although the evaluation is based on the same data used for parameter estimation. Therefore, the results demonstrate internal reconstruction performance rather than independent predictive ability. This limitation should be acknowledged explicitly in the Conclusions.
Citation: https://doi.org/10.5194/essd-2025-820-RC2
Data sets
Global marine photosynthesis parameters dateset Žarko Kovač et al. https://zenodo.org/records/17973417
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