Dear Dr Rincon-Tomas

Thank you for responding to reviewer comments. I would like to invite you to submit a revised manuscript which pays full attention to all reviewer comments. An additional review was received after the interactive discussion had closed. I attach it here, and I would like you to attend to these comments as well. Please note that the additional reviewer comments as well as your response to them will become public should you paper be accepted finally for publication.

If you have any questions please let me know.

Best regards,

Clare Woulds

Dear Dr Rincon-Tomas

Thank you for submitting your revised manuscript. I would like to request some additional changes, many of which aim to ensure that the reasoning you provide in response to reviewer comments is actually included in the manuscript discussion. Please could you therefore undertake further revisions to accommodate the comments below.

Best regards,

Clare Woulds

You mention twice that the aim of the study was to ‘...address the linkage between CWCs and present day formation of MDACs.’ The fact that two reviewers have questioned the study objectives / hypotheses supports my feeling that the phrase ‘address the linkage’ is not sufficiently explicit. Please re-phrase your aim and research questions in plainer language, and state the hypothesis that you were testing.

Please ensure that the answer to reviewer 2 point 19 is included in the discussion, with appropriate acknowledgement that the tissue you analysed was not living biomass (i.e. coral polyps), that analysis of such live tissue would be required to draw firm conclusions that methane C was not a major dietary C source, and stressing that the conclusion that can be drawn is that methane C was not a major C source during building of the exoskeleton. I recognise your point that if the corals were using methane derived C, then when it was metabolised some of it may be incorporated into the exoskeleton. However, the lack of (much) evidence for this is a rather tenuous way of drawing a conclusion about how the corals fulfilled their metabolic needs.

Likewise, please include the response to reviewer 2 point 2o in the discussion.

Please ensure that all responses to reviewer 3 are also included in the text.

Line 53 – ‘Supports’ should be replaced with ‘suggests’.

Please add a table, referred to in the opening paragraphs of the method section (therefore Table1), detailing study site lat and long, depths, and number of samples of each type collected. Please also indicate the number of replicate samples of each type collected at each location.

Please add identification of internal and external standards used for GC and isotopic analyses, as well as indications of precision for quantification of lipids and isotopic ratios.

Line 413-end of discussion. Your hypothesis regarding a biological buffer requires further discussion and possibly evidence. The two questions that occur to me are: 1) Is the presence of sulphide and methane normally prohibitive to the existence of CWCs? At what concentrations do they become problematic? Sulphide is of course toxic at certain concentrations, but non-chemosynthetic ‘normal’ or ‘background’ benthic fauna can and do inhabit sites with some level of sulphide flux (see Bell et al. 2016, Frontiers in Marine Science), and methane is even less of a problem. 2) Do you have evidence (i.e. porewater and bottom water methane and S- concentrations) to show that bacterial activity does indeed lead to reductions in sulphide concentrations such that they allow colonisation by CWCs? I’d suggest that there is another explanation, which is that CWCs are tolerant to some extent of sulphide and methane fluxes, however sulphide and methane may cause some degree of stress, which may at least partially explain the poor health (low abundance of living material) that you observed.

Dear Dr Rincon-Tomas

Thank you for your further revisions, I am satisfied with nearly all of them. I would like to seek further action on two points.

Firstly, Table 1 is very enlightening. Could you please confirm for me, are your conclusions about the C sources utilised by the corals based only on sample D03-B1, or do they also use data from other carbonate samples, which elsewhere in the manuscript are also referred to as coral skeleton?

Secondly, I do not feel that my comment about your proposed biological buffer has been fully answered. I am happy with the statement that 'These microbes may form a biological buffer...', however I am not happy with the stronger statement starting 'This model explains the observed co-existence of ...' I do not feel that other explanations (such as coral tolerance of sulphide etc.) have been fully discussed. Please either moderate and shorten section 4.3 (it would be acceptable if limited mostly to the first paragraph), or provide substantial additional argument, support from the literature, and description of patterns in your own data which support the hypothesis.

If you have further questions please let me know.

Best regards,

Clare Woulds

Dear Dr Rincon-Tomas

Thank you for these final edits, I am now happy to recommend publication.

Regards,

Clare Woulds