Dear authors,
Your manuscript has been peer-reviewed and both reviewers expressed serious concerns. Not only the way the data are presented but also the actual analysis as well as the interpretation of the results need major improvement. If you were to decide to address the comments by the reviewers in detail and to submit a revised version of the manuscript, please be aware that it will have to undergo further review.
Best regards

I have reviewed the revised version and accompanying reply to reviewers’ comments and asked a third party to look at it as well. We agree that the additional improvements are needed still. Since the topic is interesting and fits well the special issue, I am willing to consider a second (final) revision.

Both reviewers raised the issue of not having all zooplankton groups included. Authors’ reply that these groups were not part of the analysis but can be found in other papers is scientifically not strong. It is for the reader of the paper unclear why these were left out and the focus was only on the ciliates. Why were these data not requested from partners in this mesocosm study, to be included in the analysis in the current paper? The focus is different than the paper(s) referred to, and as such would produce a nice complementary study.
The goal that communities are studied does not hold by excluding important groups such as the heterotrophic dinoflagellates.

Not estimating carbon biomass (as strongly argued for by Ref #1) because of time constraints is not a good argument for a paper with the objective to look at zooplankton community and species/taxon in response to CO2 enrichment. This aspect is very important for answering the research question, and needs to be addressed/discussed. Best would be to include size/biovolume after all. Either way, please check current conclusions and edit (toned down) where needed; holds in particular for conclusions on zooplankton biomass development and carbon flux.
There is the issue of plotting against temperature instead of Chlorophyll because Chl was not found significant. This needs improved discussion why it was not significant, and please include more/clearer discussion as to how the authors this affects the results (since succession of the predators depends on changes in prey community and growth, and predation pressure by higher trophic levels). How do the temporal changes in zooplankton relate to CO2 elevations, i.e. the goal of this study?
The predator-prey relationships form an important aspect and actual grazing rates are available from other partners in this project. These may provide arguments in favour or against conclusions currently drawn from correlations in the revised manuscript.

The Discussion on predator-prey relationships deals largely with the earlier finding that the microbial loop is of particular importance during the summer (at present only reference to older publications while the current special issue has papers dealing with this topic; I recommend to include those as well).
The authors do include in the revised manuscript discussion on the paper referred to by Ref #2, however, the comments by Ref #2 are more general: enhanced flow through the microbial loop tends to decrease food web efficiency. This needs to be addressed better (check also papers on topic in the current special issue).

Some other points:
1) Please indicate in the reply to reviewers what exactly has been edited/changed and state page and line numbers of the revised manuscript (this holds for the original as well as the current review comments).
2) Check whether all points raised by reviewers are considered and state clearly why what has been done to address them (e.g. not all general comments by Ref #1 were addressed).
3) Some figures still state microzooplankton instead of ciliates.
4) State genus/species names italic (e.g. Tables).
5) Please provide the correct information when referring to published papers by partners in this field campaign; e.g. Picoflagellates in the paper of Crawfurd et al. (special issue) are not all flagellated and should instead be cited as originally stated (picoeukaryotic phytoplankton, Picoeuk I etc.).

Authors have taken into account Reviewers' comments and suggestions.