Dear Itay Bar Or and co-authors:

Thank you very much for submitting the revised version of your manuscript and your response letter. Both reviewers found merit in your study, but also raised some serious concerns.
Now your manuscript has improved substantially, but I would still ask for some minor corrections (see below).

I will be happy to accept a second revised version of your manuscript if you address all suggestions.

With best regards


Kirsten Kuesel
(Co-Editor of Biogeosciences)



Main comments:

1) The archaeal sequences belonging to uncultured lineages (MCG, MBG-B, MBG-D) represent less than 5% of the sequences. It is impossible in this case to infer on their potential metabolisms based solely on the geochemical characteristics of the environment in which they were detected. I would suggest deleting all paragraphs pertaining to these groups in the discussion and discuss the dominant archaeal groups which are also known described cultured organisms.

2) Part 4.2 is long and descriptive, whereas part 4.3 contains very interesting information. Please delete part 4.2 and integrate the most relevant data from this part in part 4.3.

3) Most of the discussion in part 4.3 needs to be checked for English and the authors need to clearly write what data type they are discussing. Here are some examples:
L. 543 states ‘mcrA functional gene of methanogens/anaerobic methanotrophs shows’, which should be written ‘xxx analysis of mcrA functional genes … shows’.
L. 546-548 ‘is likely because that the mcrA observed …’, what are the authors referring to here? qPCR data or mcrA gene sequences?
L. 547 ‘methanogens which maybe cause the reverse methanogenesis’, methanogens possibly perform reverse methanogenesis but they don’t cause it.
Etc …

Specific coments
L. 82 : Please change ‘microbial pathways’ to ‘microbial communities’
L. 187: ‘Chimeras’?
L. 266-271: This paragraph has information that is repeated after in more detail, please delete. Same comment for paragraph L. 280-286.
L. 285-286: Recent data suggests that the MCG and MBG-B are separate phyla and are not considered to belong to the Thaumarchaeota anymore. Hence some of the further discussions need to be amended.
L. 304: MBG-D and DHVEG-1 belong to the same cluster, they can all be labelled MBG-D.
L. 384-385: please explain this sentence, what was analysed exactly?
L. 403: ‘microbial populations’, ‘methane cycling’
L. 515-517: ‘which creates … in deep sediments’, please rewrite this sentence.
L. 526: there is a verb missing in this sentence.
L. 533: ‘can occur by one microorganism?’ Please rephrase.
L. 534-536: 16S rRNA gene data is not enough to infer on metabolism. Please delete this sentence.

Dear authors

Thank you for the minor revsions. Thus, the revised version of your manuscript can be published in Biogeosciences without further delay.

Your interest in publishing in Biogeosciences is very much appreciated.

Sincerely,

Kirsten Küsel

(Co-Editor)