Comment on bg-2021-113

This paper investigates the seasonal cycle of nearshore phytoplankton in the Peru Upwelling System (PUS), one of the richest upwelling systems in terms of fish catch. The PUS is particular as the surface chlorophyll seasonal cycle is out of phase with the winddriven upwelling intensity, suggesting that vertical mixing may generate dilution and lightlimitation. The paper is structured in two parts: first, the surface chlorophyll, nutrients, mixed layer and upwelling rates of the PUS are compared to those of three other EBUS (California, Canary, Benguela) using observations. Second, a regional coupled physicalbiogeochemical model (CROCO-BioEBUS) is set up for the PUS and used to study the limiting factors of phytoplankton growth and to perform a phytoplankton budget in the mixed layer.

Besides the nicely presented figures and the english that needs to be thoroughly corrected, I was disappointed by the results presented in the paper. First, the authors do not really do justice to a previous paper (Echevin et al., 2008, hereafter EC08) that investigated exactly the same questions using a quite similar modelling approach. The latter is barely cited in the introduction and discussion, even though these authors conducted a comprehensive investigation of the factors driving the seasonal cycle of chlorophyll. As a co-author of this latter work, I was curious to find out whether some new questions or new approaches regarding this paradox were being investigated. Unfortunately, the material presented in this work provides very little new information with respect to the findings of EC08. The authors could have used their model to perform innovative sensitivity experiments (for example EC08 performed several sensitivity experiments to illustrate the impact of iron limitation, temperature, insolation on the seasonal cycle of chlorophyll) but here only one model experiment is analyzed. They claim that they elaborate on the propagation of the seasonal cycle of surface chlorophyll onto higher trophic levels, but very few results are presented in the manuscript. The second part of the paper, which compares different EBUS systems, is not particularly innovative in comparison to previous findings of Messié and Chavez (2005and Chavez ( ,2015. It seems that the authors were inspired by these previous works but did not manage to expand on the scientific questions. For this reason, I think that the paper in its present state is not worthy of publication in Biogeosciences Discussions.

Introduction
L33-35: The seasonal paradox is also mentioned by EC08. At citing the latter, it would be fair to mention that they used a regional coupled physical-bgc model as in the present study. You should also mention Thomas et al. (2001) and Chavez et al (2005) who noted the seasonal paradox.
L38: Actually EC08 showed that the seasonal cycle of insolation did not play a major role in their model set-up, whereas Guillen and Calienes (1981) assumed it played a role.
L39: I disagree here: this has been at least partly assessed in EC08. Rephrase and explain precisely which hypotheses have not been assessed in the latter and which new ones will be assessed in the present work. Overall, a more accurate review of the findings of EC08 to explain the out-of -phase seasonal cycle of chlorophyll is needed in the introduction. L41: "the unique mechanism": not clear what this unique mechanism is. L43: use present tense.

Data and methods
L50: why do you cite ROMS here? Explain that CROCO is the next generation ROMS-AGRIF model.
L54: "which is used in this study": suppress this part of the sentence. Both grids are used in the study but only the results from the fine resolution one are analyzed.
L54: do you use bulk forcing? L61: I think the authors should explain why these variables are important for the simulation of chlorophyll. Figure 1 of José et al shows that the PCC is too strong in the model at 12°S, not too weak! L66: I do not think it can be said that N is a species. I think the authors could have done a better job at proofreading the english in the submitted paper.
L72: Table A1  L73: Good to know that the model has been adjusted to fit zooplankton biomass, which to my knowledge, has not been done before: which figure and section is it? Figure C1: I think showing N at ~100 m is more relevant than at 1000m, as it would be in the depth range of upwelled waters. Besides, N at 1000m is not at quasi equilibrium after 25 years, it is still drifting quite a lot.
L79: "where shows..": rephrase. L81: I am not sure the title of the subsection is adequate. I suggest "Model diagnostics".
L82: "analyze with...": another typo. There are too many of them, the language really needs to be corrected, I am sure the authors can do a better job at it or get some help from a native speaker.  L145-146: I do not agree with the conclusion here: as SST is also strongly correlated with insolation, you can not conclude that the seasonal cycle of temperature drives the phytoplankton growth. For your information, EC08 showed that the temperature effect was negligible in their model set-up (see end of section 3.3). L150: The reason for this is well known: the along-shore wind forcing is enhanced during winter, increasing upwelling and vertical mixing, and the lower winter insolation decreases surface stratification and increases the MLD. L181: "DV contributes...": in which figure is this shown? L206: "advection is picking up": I can not see that, advection seems negligible with respect to mixing (Fig.4d). L208-209: "the decreasing rate...": I do not understand this sentence L202-2011: This paragraph is very difficult to follow and lacks precise references to the figures in the core of the text.
L222: How do you obtain this 60% decrease based on Eq.3? L229: The weak role of temperature is in agreement with EC08.

Discussion
L258-261: I suggest a closer examination of EC08 findings and expand the comparison with their modelling work, which is very similar to what is presented here. In particular, they relaxed iron limitation in their model and found an Chl increase of 20-80% (depending on the latitude) during winter and spring, which corroborates the impact of iron limitation on the seasonal cycle found by Messié and Chavez (2015). L272: the sentence seems incomplete.
L274: "and in deep ...": rephrase L275: "charge" L276: I am not convinced by this hypothesis: the residence time of the upwelled water in the mixed layer near the coast is probably quite short as upwelled waters are rapidly transported offshore by Ekman currents. Thus I do not believe in such preconditioning. Unless you can you prove it using the model. L295: "higher" with respect to what? Clarify.
L314: is this a result of the study? It has not been described. I think elaborating on the seasonal cycle of export and zooplankton could have been interesting. L320-332: This discussion is very speculative and vague. I do not find it very useful. L340: Echevin et al. (2020) also investigated the mixed layer evolution under climate change (Figure 7), not only changes in upwelling. I encourage the authors to read the papers they cite more carefully.
L355: The propagation of the seasonal variability up the foodweb is not documented in the results sections and only mentionned in the discussion: it is not worth mentioning in the conclusion.