the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
PIBM 1.0: An individual-based model for simulating phytoplankton acclimation, diversity, and evolution in the ocean
Abstract. Phytoplankton is a diverse group of photosynthetic organisms and accounts for almost half of global primary production. However, most existing marine ecosystem models incorporate limited phytoplankton diversity, overlook phytoplankton evolution, and treat phytoplankton as concentrations instead of particles. Here we present an individual-based phytoplankton model that captures three dimensions of phytoplankton traits (size, temperature, and light affinities) and allows phytoplankton cells to mutate in a one-dimensional (1D) water column. Other components of this ecosystem include dissolved inorganic nitrogen, twenty size classes of zooplankton, and detritus, all modelled as Eulerian fields. This hybrid plankton model can reproduce the general seasonal patterns of nutrients, chlorophyll, and primary production in the subtropical ocean. We expect that this model will be a useful tool for studying phytoplankton physiology, diversity and evolution in the ocean.
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Status: open (until 13 Dec 2024)
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RC1: 'Comment on gmd-2024-130', Anonymous Referee #1, 18 Sep 2024
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The comment was uploaded in the form of a supplement: https://gmd.copernicus.org/preprints/gmd-2024-130/gmd-2024-130-RC1-supplement.pdf
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RC2: 'Comment on gmd-2024-130', Anonymous Referee #2, 12 Nov 2024
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# ReviewIn general, individual-based phytoplankton model is a promising topic. The authors built a vertical-1D NPZD model at BATS, in which only "P" is individual-based. Though building a model from scratch involves a lot of work (and I value the efforts the authors put), sometimes it's actually not necessary cause there're already models available to use to answer research questions the authors wanted to ask (and probably better in performance and easier to use). For example, models developed by Hellweger's group (e.g., Hellweger et al. 2014, Science, mutation is included) and PlanktonIndividuals.jl (https://github.com/JuliaOcean/PlanktonIndividuals.jl, developed by MIT Darwin Group, the model resolves intracellular macromolecular composition of multiple species). Personally, I think collaboration with these groups is actually more efficient than building a model from scratch. Anyway, there's nothing wrong the authors chose to build their own model. But I still have some question and comments for the authors before moving forward to publication.## Specific comments- Line 20: This is true, but only 20000 particles still cannot represent the full distribution of phytoplankton community. It's too low compared to the real cell density.- Line 23: Lagrangian phytoplankton model may also not be the ground truth.- Line 45: This is not true. PlanktonIndividuals.jl as mentioned above, also developed by Mick Follows' group.- Line 74: a constant number of super-individuals with each super-individual represents a flexible number of cells VS flexible number of super-individuals with each super-individual represents a constant number of cells? Actually I prefer the second one. Here's the reason, the first one sounds like an assemble of many tiny 0D Eulerian models and cell division is actually a change of concentration not number of cells.- Eq.3: I don't think respiration cost Chla.- Fig.4: There're still considerable discrepancies between simulations and observations. For example, the deep chl maximum and the depth of NPP. I'll put a question mark on the choices of parameters.- Line 535: As mentioned above, 20000 particles may still not be enough.- Section 4.1 and 4.2 should be shortened and go to Introduction.Citation: https://doi.org/
10.5194/gmd-2024-130-RC2
Model code and software
PIBM 1.0.2 code Bingzhang Chen and Iria Sala https://doi.org/10.5281/zenodo.12702990
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