Dear Dr. Sreeush,
I have read the answers that you have provided to the comments of both reviewers. Based on that, I encourage you to submit a revised version of your work that takes into account the modifications mentioned in your answers. For the clarity of the manuscript, please define very carefully the definition of the compensation depth that you chose for your study and justify this choice very clearly (as you did in your answers to reviewer 2).

Many thanks in advance for your efforts,

Kind regards

Marilaure Grégoire, associate editor.

Dear Dr. Sreeush,
I have read the revised version of your manuscript and based on that I find that major revisions are needed for the following reasons. In its present form, the manuscript is still difficulty understandable for a general reader not experienced with the type of models used for OCMIP. Since the beginning, I was wondering why the compensation depth is not dynamically computed by the model then I had to read Najjar and Orr, 1992 to understand the approach. Therefore, I suggest that you clarify since the beginning the general approach of OCMIP modeling e.g. a simple biological model with a reduced number of state variables without an explicit representation of chlorophyll like in mechanistic models because…). It can be done briefly already in the introduction and then clearly in the methods section. In addition to the general approach, I also find that the description of the model is insufficient. The information provided does not allow to understand the approach (even the basics). I would start the material and methods section, by informing the reader on the structure of the biogeochemical model (a scheme would be helpful), listing the state variables and interactions between them, mentioning that these variables are transported by a 3D physics. For instance, a synthesis of section 7 of the paper by Najjar and Orrr, 1992 would really help the general reader to understand the modelling approach (see also my detailed comments below).
I still have concerns about the definition of the compensation depth made in the manuscript and how it translates in terms of model formulation and validation. You decided to define the compensation depth as the depth at which the community respiration equals photosynthesis but then after I noted some confusions that need to be clarified : 1) you mention that at the compensation depth, phytoplankton production is zero, which is not true (lines 112-115 ), 2) in the model formulation, you consider that below Zc, there is no biological production (Jprod=0), 3) model estimations of biological production are compared with vertically integrated primary production over the euphotic zone as proposed by Behrenfeld and Falkowski (1997). It would be helpful finally that you clearly define as early as possible the biological production (most of the time it is photosynthesis which is not the case here).
I thank you for your efforts in incorporating my comments.
Kind regards,
Marilaure Grégoire, associate editor.

Detailed comments:
Abstract: Lines 27-28: “Utilizing the principle of minimum solar radiation for the production zone..” What is the principle of minimum solar radiation?
Lines 112-115: I do not agree that if the irradiance is less than Ecom, phytoplankton growth will be negative and hence phytoplankton will decline due to respiration. This would be true if Ecom represents the irradiance at which photosynthesis equals autotrophic respiration. I would like that you clarify that point. Besides, clarify what you mean by “the growth will be negative” . Growth of? (line 113).
Line 116: please define what you mean by “oceanic production zone”.
Line 121: please avoid parentheses insides parentheses.
Line 127: please define “optimum” solar radiation? What do you mean by optimum? How variable will be the surface light? And which data do you use? Please specify
Lines 127-129: This sentence is not clear and needs to be reformulated. First a reference is needed for justifying the choice of 10 W/m2 for the value of the compensation irradiance. Then, the second part of the sentence “…and calculated its depth…” needs to be reformulated. Do you mean that “ a spatially and temporally varying compensation depth is estimated from a vertical light profile taking into account the shading effect using a typical? Chlorophyll profile. Please specify how the chlorophyll profile varies in space and time?
Line 141: please clarify what do you mean by “positive” effect? Better representation?
Line 161: why “respectively”?
Lines 163-179: Please specify that all the details that you are giving concern the biogeochemical model and if the model is solved on the same grid as the physical model. At the beginning I thought that it was for the physics and was wondering why all these details are given since you did not run the physics but rather force it from another simulation.
Lines 180 -: Conversely, I would like to have further specifications on the biogeochemical modeling approach since the OCMIP-II protocol is not known by everybody. I think that the description of the approach that you gave at lines 181-183 is not enough for understanding the methodology and in particular, how it differs from “classic” biogeochemical modelling approach. You mention a restoration to ocean biology (which biology) and appropriate biogeochemical parameterization. Please give more details and give a reference with the methods is described because as it is, this is not enough to understand what is done.
Line 184: what is the first order carbon cycle?
Line 185: “explicit ecosystem models” please specify. I guess that it is the classic modeling approach but as said before, due to the lack of details we cannot understand how you approach differ from this “explicit” approach. Do you mean models that explicitly solve the light profile? Your model is also explicit for certain variables.
Line 191: phosphorus and not phosphate
Line 202: Since as far as I understood you did not run the physics? If yes, I would move what concerns the physics to this section and leaves to the model section what concerns the biology. Besides, you mention that you use ocean reanalysis products, is it for the physics only or do you use them for restoring the biology? For the remaining of the manuscript, I guess that this reanalysis is only used for the physics and so I do not see why we need to describe twice. Please clarify
Lines 208-210: Please reformulate. The initial conditions for PO4 and O2 were taken from World Ocean Atlas 208 (Garcia et al., 2014) while for DIC and ALK data from the Global Ocean Data 209 Analysis Project (GLODAP; Key et al., 2004) are taken. What about DOP? Oxygen is not listed as a state variable in the appendix so why do you need to initialize it? You mention a list of data for validation like satellite estimated NPP, how do you link with model?
Line 219: please add a reference.
Line225-227: Please reformulate. “ This includes anthropogenic increase…” what represent “This” this is not clear what includes anthropogenic DIC?
Lines 228-229: please clarify the aim of these sensitivity experiments directly (you want to remove the effect of upwelling). . You remove the seasonal cycle form the physics and only impose that from Zc? (we understand afterwards reading the results section ).
Line 265-266: “the model permits 100 % relative photosynthesis for radiation above 50 W/M2” what do you mean by relative photosynthesis? from equations given in the appendix, no term related to photosynthesis is presented. Do you mean Jprod is not null when the irradiance is above 50W/m2(so when Z Line 268-269: clarify the link between phot inhibition and phosphate availability as it is not clear how the availability of phosphate can be linked as a general rule with photo inhibition.
Lines 235-238: this part is not clear. What does “x” represent and reformulate.
Line 241: compensation depth is already previously defined. Once defined, Zc should be used throughout the manuscript.
Line 252: Same remark as for Zc for varZc
Line 262: the average relative photosynthesis needs to be defined and details on how it is computed need to be provided.
Line 272-273: Please reformulate, this sentence is heavy. Consider for instance: “The value of Zc estimated from equation… shows marked seasonal and spatial variability (Figure 3). ..
An equation stating clearly how Zc is estimated would help.
Line 275: “..and deepens up to 45 m from March to May due to the increase in the surface solar radiation”.
Line 278: Zc and not “the Zc “
Line 281: Please replace compensation depth by Zc and do it through the manuscript for consistency.
Line 282: Zc and not “the Zc”
Lines 283-286: Please explain how these factors can affect the penetration of light. If it is through chlorophyll, this is taken into account since in your profile you use a chlorophyll profile from the observation. Turbidity? Please clarify the link or remove.
Line 299: Please clarify what does mean “optimum” here. Surface value? If yes this is not optimum.
Line 299-300: reference to Parsons et al 1984 is for the parameterization used for Zc? If Yes you do not need to remind it here again (better to do in the description of the equation above) because it is confusing as we can wonder whether this reference to Parson concerns the fact that the production zone is never larger than 75m.
Line 300-301: “The consequence of this on the seasonality …”. The consequence of What? A varying Zc? Or a Zc limited to 75m?
Lines 306-307: How pCO2 is derived from your model state variables? Give a reference in the modeling section.
Line 316: please explain how the new production is estimated from the model? Jprod converted into carbon? This is confusing because at line 702-703, it is mentioned: “ the biological production in the model Jprod is calculated using equation A1” then lines 730-731: “… the rate of change of phosphate which represents biological production in the model …”. However, the rate of phosphate change (see eq A3) also incorporates some remineralization of DOP and hence is not only linked to “primary production”. As far as I know new production, is the production based on “new nutrients” (and not remineralized nutrients).
Line 378: Please explain how the export production is estimated from satellite estimated vertically integrated production over the euphotic zone and how this can compare with the model estimated production over the compensation depth.
Line 375: what do you mean by “new biological parameterization”? Are they related to the model that you described in the appendix? Or is it the use of varZc? In that last case please mention the use of VarZc as this is how it is referred in the text. I find that using biological parameterization is confusing.
Line 363: fails or simulations
Line 380 simulations or has
Line 408: please explain how Fig 8d shows that the simulated export production is consistent with satellite data.
Line 410-411: Tables 1-4 summarize
Line 413 strengthened
Lines 570-571: please explain how temperature affects your biological model? For appendix this is not explained.

Appendix: the description that is made is insufficient. Please provide the evolution equations for each of your state variables (i.e. DIC, ALK, PO4, DOP, O2?).
Line 701: As far as I understand, JDOP, JPO4 represents the balance between sources and sinks while Jprod and JCa represent biogeochemical flows with respectively production and calcification, so J is not always the balance between sink and sources.
Line 703: please define precisely what is meant by biological production.
Line 706: please clarify in equation A1 that when the phosphate concentration is lower than the climatology, there is no production.
Line 707: “a fixed fraction of production” rather than “ a fixed fraction of phosphate”, “a source for DOP”
Line 708: phosphorus
Line 709: remaining is (1-sigma) Jprod nd not kappa*[DOP, Kappa*[DOP] is remineralization.
Line 728: What does phi represent? In the main text, eq 1 states that phi represents the production/destruction term? In the appendix, we are told that J is the production/destruction term and here what does phi represent?
Line 732: the value of Rc:p is inconsistent: here Rc:P equals 117 while at line 720 this ratio equals 106.
Line 733: Phi needs to be defined. At line 171, phi is defined as a source/sink term. Now J is used to define that term.

Figure 3: Seasonal maps of the compensation depth estimated from equation (give the number of the equation) … …Please explain what is the blue rectangle in Figure 3a.
Table 4: I guess that it is model derived values and not satellite derived values

Dear Dr. Sreeush,
I have read the revised version of your work as well as the answers you provided to my comments. I find the manuscript much improved but I still have comments.
I have problems with the title, “Optimization of Biological Production for Indian Ocean upwelling zones: Part – I: Improving Biological Parameterization via a variable Compensation Depth” because the paper is not dealing with optimization of biological production (better estimation but not optimization). I would suggest something like “Biological production in the Indian Ocean upwelling zones: Part –I: refined estimation via the use of a variable compensation depth in ocean carbon models. “ it would more reflect the content of your paper.
I also find that the paper is very long with notably 8 tables and 21 figures which may render difficult to capture the main messages. I would suggest that you consider to put some figures as supplements and that you leave in the main text the most striking ones.
In addition, please see the minor comments here below.
Thank you for your efforts,
Kind regards,
Marilaure Grégoire, Associate Editor.

Comments:
In your answer to my comments, you mentioned that biological production will be defined in the text (you mentioned lines 729-730 but it is not the case. So please define biological production since the beginning (Introduction). For instance (Lines 123-), when you defined Zc, it will be appropriate that you inform the reader on what will be the biological production in this manuscript.
Lines 154-155 : Please reformulate.
Line 221-223: Please refer appropriately to appendix for details on the model equations, Line 226 : Jprod has to be defined.
Lines 226-229: I suppose that Jrpod =(2) if PO4>PO4* and Z While Jprod=0 if PO4Zc? Please clarify as it is not clear if the two conditions are needed or not. (it is needed at line 227 while at line 229 it is one of the two if I am right)
Line 283: suppresses
Lines 294-304: Zc, NPP,.. have already been defined before in the introduction (lines 107-123)
Line 320: Why 50 W/m2? Equations (2) suggest a difference for Z Line 745: “are” the biological source/sink terms..
Line 746 “ due to evaporation..” do you mean air-sea exchange?
Lines 750-753: you use JDOP, JPO4, JDIC, JALK while above you use JbPO4,JbDOP,.. please homogenize the notation for clarity.
Line 764: JDOP, ..already defined above
Line 801 remove “is” because it is written twice.

Dear Dr. Sreeush,
I have read the revised version of your manuscript and I found that you have addressed all my comments. I am thus pleased to accept your paper for publication in Biogeosciences provided that you address the minor comments here below.
Thank you for your efforts for taking into account my comments,
Kind regards
Marilaure Grégoire

Minor comments

Minor comments
Line 158 U and W are the velocity (please add W as in the equations below)
Lines 188-189: I would say “Inorganic phosphorus”
Line 203 : how Jprod can give a new-production in gC/m2/yr ? you need to have a conversion factor from phosphorus to carbon.
Line 283 : why did you mention (“see Appendix 2”) ? Figure 2 is not in the appendix
Lines 330-331 : the order of presentation of case study is firt SC and then SCTR.