Dear Dr. Moreno,
Your manuscript has been evaluated by two external reviewers. Based on their review and your answers to their comments, I invite you to submit a revised version of your work. The revised version has to incorporate all the changes that you mentioned in your answers to the two reviewers’ comments. In particular, it is important that this revised version addresses the serious concerns mentioned by reviewer 1 on how your approach is appropriate to infer the processes that explain the variability of POC and the impact of ocean acidification on plankton communities. It is therefore needed that you justify the design of your study in relation to the main aim of your manuscript. Results of your work demonstrate that variability in initial conditions may induce a variability in phytoplankton dynamics comparable or higher than that observed in different CO2 treatments. Reviewer 2 would like you to comment on practical recommendations that can be made for the design of future (mesocosms) experiments dealing with the assessment of the impact of ocean acidification.
Thank you for your efforts,
Kind regards
Marilaure Grégoire

Dear Dr. de Castro,
One of the reviewers has assessed the revised version of your manuscript, " Potential sources of variability in mesocosm experiments on the response of phytoplankton to ocean acidification", and your response to his/her comments. I have also read that revised version. Based on that, I suggest that your manuscript be accepted for publications in Biogeosciences provided that you take into account the minor comments which are at the end of this letter.

Thank you for submitting your manuscript to Biogeosciences.
With kind regards
Marilaure Grégoire

Minor revisions:
I would recommend that you define more clearly the meaning in your paper of (ecophysiological) “uncertainty” (uncertainty is defined on page 3, line 28 but I suggest that you clarify that, in this paper, this relates to the random variations in the initial conditions of the experiments (if I understood correctly), “variability”, “sample/replicate”, factors, ..already in the Introduction. I agree that some of these terms are defined afterwards in the material and methods section but some specifications of their meaning in this paper would be helpful in order to understand the introduction and, in particular, the objectives on of the study. Indeed, I find that, as it is now, the description of the objectives of the manuscript (page 5, lines 4-16) is still not straightforward to understand especially for a general reader, although these lines are important as they define the scope of the paper. For instance, you mentioned: “In this study, we estimate the effects of ecophysiological uncertainties by associating the variability in experimental observations to a variational range from repeated model runs”. This sentence is very technical (especially its second part when you are not an expert and when you have not read the whole manuscript). I would suggest some reformulations. For instance (but it can be of course different), “We estimate the effects of ecophysiological uncertainties (i.e; different initial conditions in a selected number of factors …) on the variability in experimental observation (here the POC variations). With that aim an ensemble of model simulations starting from a range of selected factors is performed. The range of selected factors is defined so as the variability (i.e. standard deviation) of model outputs does not exceed that of experimental data during the course of the experiment”.

Dear Dr. Moreno de Castro,
I have read your revised version of your manuscript and I am pleased to accept it for publication in Biogeosciences.

Thank you for your efforts and for having submitted your manuscript to Biogeosciences.

With kind regards,
Marilaure Grégoire