Dear author,

Your responses have addressed most concerns and comments from reviewers and editor.

Please go ahead to re-structure your manuscript and do stay focused on the key point about AOM, i.e., the background, the biomarkers, the novelty and the implication of your AOM in this study.

Best wishes

Zhongjun

Dear Prof. Shin,

Thank you for resubmitting your manuscript to BG.

I had an editorial review and found that the new version has been much improved, but there are still questions that need to be addressed. Thus, I am returning your manuscript for minor revision

The key concern I would like to point out is that the writing of abstract. Please remove the statements that might be controversial, and that are not widely accepted. For example, phylogenetic analysis of 16S rRNA gene could be considered as the ultimate evidence for the presence of ANME, but the ratio of of sn-2-hydroxyarchaeol to archaeol (>1) might not be that conclusive. In addition, the general term ANME-specific lipid could be used rather than sn-2-hydroxyarchaeol in the abstract, unless these lipids are solely detected in ANME. In the introduction and discussion, the authors can then discuss the advantage and disadvantages of these lipids as biomarkers of ANMEs. In a word, one has to bear it in mind that sequencing analysis of 16S rRNA genes is more conclusive evidence than the lipid-based chemotaxonomy.

Thank you for submitting your paper to BG.

Sincerely,

Zhongjun JIA
Minor comments
(1) L34-36. How confident the authors are by pointing out that these sn-2 and sn-3 hydroxyarchaeol are ANME-specific biomarker. If it was also detected in some of methanogens, the authors might have to rephrase these sentences.
(2) L36-37. I guess phylogentic analysis alone is sufficient to claim that ANME-2c and 3 are the predominant methane oxidizers. The ratio of sn-2-hydroxyarchaeol to archaeol may not be that conclusive.
(3) L42. Please conclude the abstract by stating the importance and/or implication of this study, but not the perspective for future study. For example, these results suggest that niche diversification of active mud volcanoes has shaped distinct archaeal communities that play important roles in anaerobic methane oxidation and organic matter turnover in Beaufort Sea.
(4) The redundant description? i.e., The content of L53-56 appears to be similar to that of Line 60-63.
(5) L66-67. There is no necessary to cite 6 different references for a simple statement. Please delete some
(6) L107. by using a combination suite of lipid and nucleic acid analyses...
(7) L213. Please specify the samples used for DNA extraction
(8) L257, Please indicate that these archaeol can be considered as the biomarker for ANME.
(9) L281. Rephrase as “Depth profile of archaeal communities”
(10) L282. It can be rephrased as following: Archaeal communities were phylogenetically classified as the taxonomic level of class
(11) L326. Do the authors determine the concentration of others electronic acceptors such as Mn and Nitrate and Fe?
(12) L331. One cannot get a clear idea of this section,. i.e., it the AOB biomass contribution to TOC is low, so what?
(13) L347. In the result section, please briefly mention that these non-isoprenoid DGD could be considered as a potential marker of sulfate-reducing bacteria
(14) L385. Delete and referneces therein. It has been mentioned
(15) L391-396. It seems contradictory to some extent. For example, In the abstract, the authors claimed that both sn-2-hydroxyarchaeol and sn-3-hydroxyarchaeol are representative of ANMEs, But in this paragraph, it appears that these archaeol could be found also in methanogens. The question is how specific these biomarkers for ANMEs
(16) L399. Does this mean that sn-2-hydroxyarchaeol is a better indicator for ANME-2, while archaeol can represent ANME-1 much better?
(17) L453. MCG group now refers to Bathyarchaeota ?
(18) L466. at a site?
(19) Fig.1. please provide the full name of mbsf
(20) Fig.5. if flexible, please add the bootstrap value of >70 on the tree