Dear Inga,
many thanks for your responses to the referees’ comments.
Before, sending out your manuscript for review I sent the paper for a quick access review in order to ensure that the paper is correctly understood as what it is. Obviously, the concern was not unfounded because still one of the reviewers (a highly valued expert) reacted quite negatively. I tend to agree with reviewer#3 in many aspects, but I do not think all points can be clarified in one single paper and in some way this person seems to ask for a lot – and maybe too much. The last point of reviewer#3 is a serious one and should be considered in any case: “One thing the authors could do is make a table of all of the processes they discuss, and rank their importance in terms of future model development by criteria that are clearly stated and applied consistently. This might lead them towards crafting a sound and credible contribution.” This cannot be easily dismissed. I think the present manuscript can benefit substantially from what reviewer#3 writes. This would also protect you as authors from potential similar critics of others.
The more modest critics of reviewer#4 go somewhat into the same direction: “’: without going into ...’ This is a main explanation for the choice of the processes. I think it would deserve some more words, as for instance some feedbacks may not be known in general or not completely known to the authors.” I think this refers to your sentence (p 2 l 3-4): “Instead of improving a single mechanism, the idea is to account for ‘mechanism diversity’, without going into too much detail of one specific process at the expense of others.” This is so general a statement that it is as such not very useful. The manuscript must become more concrete here. Rephrasing the one sentence will not be enough.
Concerning the alkalinity and CaCO3 production issue mentioned by reviewer#2, the effect of dilution with freshwater or the concentrating effect of evaporation should be mentioned as well. CaCO3 production/dissolution variations may not lead to large climate feedbacks on scenario time scales, but can be critical for natural variations of the carbon cycle and climate and also on feedbacks on the long-term. Therefore - not only for this CaCO3 related example - , it is crucial to define over which period and for which problem area the model in question should be applied.
The summary and conclusion section is too concise in my view. How would look your “dream Earth system model” from a marine biologists view look like concretely? What would you suggest as next steps? The present statements such as the following one need to be substantiated by a concrete reasoning: “But in contrast to these state-of-the-art concepts, we consider important links between the marine biosphere and other Earth system components and allow in that way more important feedback loops to take place. We believe that our framework is better suited to account for possible changes in the strength of feed backs.”
I suggest that you provide a substantially revised manuscript based on all three reviews. Please, take all points of the referees thoroughly into account for this revision.
Many thanks for submitting to Biogeosciences and using the open access way for publishing. This is highly appreciated.
Best wishes, Christoph

Dear Inga,

Many thanks for your revised manuscript and the report about the changes made. I see that you have changed the text at many places. Nevertheless, I would like to kindly ask you to make a few further adjustments which should be doable in a shorter time frame.

1. Abstract:
Replace
“…enables a larger number of relevant feedbacks to take place…”
by
“…enables inclusion of the relevant feedbacks in climate change quantifications…”

2. The paper may cause different reactions to the readers depending on whether the read the paper with the eyes of a (more physical) climate modeller or with the eyes of a marine ecosystem modeller (see the spread in the reviews). Therefore, it would be good to state up-front what this paper is about.
Please, insert a sentence directly after the sub-heading “1. Introduction”:
“This perspectives paper deals with the marine ecosystem component of Earth system models and the quantification of respective feedbacks as well as impacts.” (or something along these words)

3. At end of page 1/beginning of page 1 you write:
“To consider more biological variables in models is clearly the right way forward if one is interested in the response of the marine ecosystem to climate change (see Le Quéré, 2006, for a discussion).” Can you add reasons for this? I think this issue is debated. More complex models do not necessarily provide better results, especially when many not well constrained processes are added to models. I think one needs the appropriate level of complexity tailored to a specific purpose. Ernst’s outstanding strength was to discriminate between important and unimportant processes in his modelling. Perhaps, you can add a paragraph discussing the trade-off between complexity and understanding? What use is a model that is so complex that cause-effect links cannot be anymore identified?

4. Page 2, line 8:
Replace
“...trigger climate feedbacks…”
by
“…cause feedbacks to climate…”

5. Page 3, line 8:
“Bacteria decompose the organic matter while sinking down and thereby determine the efficiency of the organic carbon pump.”
This reads as if the bacteria are sinking down; moreover bacteria decompose also non-sinking organic matter. Please, reformulate so that the meaning is unambiguous.

6. Page 3, line 9:
“The climate relevance of the organic carbon pump has been evaluated by quantifying the air-sea fluxes of CO2 without this mechanism.”
This sentence does not make sense. I know what you mean, but for the unexperienced reader this is enigmatic. Please, reformulate.

7. Page 5, line 27:
“Another important long-lived greenhouse gas is N2O with a global warming potential for a 100 year time horizon that is approximately 300 times higher compared to CO2 (Ramaswamy et al., 2001).”
This cannot be. Or I have misunderstood what you write. The specific greenhouse potential (per molecule) of N2O is larger than that of CO2, but CO2 is and will be by far the largest agent in radiative forcing. Please, correct and use the newest results from IPCC AR5.

8. Page 5, line 35:
It would be good to mention potential destabilization of gas hydrates as well as sub-seabed permafrost and the conversion of the respective CH4 to CO2 by microbes.

9. Page 6, sub-heading “3 What are the future impacts”
You motivate the paper with quantification of climate relevant feedbacks. Therefore, the “impact topic” now comes a bit as a surprise. I do not know whether “impacts” is the best word here, as it is often contrasted to feedbacks. Maybe “What are the future implications for ecosystems and climate change?” is a more correct heading.

10. Page 8, line 20:
“Nevertheless, it is expected that an expansion of oxygen minimum zones will increase the production of N2O (Naqvi et al., 2010), because the highest production rates occur at the anoxic-oxic boundary layer.”
Nitrification is named as the key marine N2O production mechanism (Freying et al., 2012, Phil. Trans. R. Soc. B (2012) 367, 1245–1255). Boundary layers are usually associated with the friction layers at the top and bottom of the sea. It is not clear what is meant with “the highest production rates” – production rates of what?
This sentence needs reformulation and correction. It may be wise to split the text into several sentences. The statements need backing by references.

11. Please, give the manuscript to a native speaker for a language check and respective improvements. The respective comment by reviewer 2 (“The English is poor…”) is not very diplomatically formulated (I know this hurts). Nevertheless this reviewer has a point and this needs to be addressed carefully.

Thank you very much for your attention. I look forward to your new version.

Best regards, Christoph Heinze

Dear Inga,
many thanks for the revised manuscript and your response about the changes made as well as your clarifications. I found one typo (p 10 l 8, "absoprtion), may be it is good to send the manuscript another time through a spell checker before you upload the final version for production. I find the paper significantly improved and think that its message is presented in a clearer fashion now. I accept your paper for Biogeosciences. Congratulations and thank you for (a) using the open access way of publishing in BG, (b) for contributing to the Maier-Reimer special volume, and (c) for your endurance/patience during the revision process! Best wishes for 2017, Christoph