Dear Aurele,

the reviewers raised major concerns regarding your MS. Though I recognise that you modified your work, I would like to have a second round of reviews and will as the reviewers to consider if modifications and your reply justify publication of your MS.

With best wishes, Helge

Dear Dr. Vuillemin,

thank you very much for choosing BG to publish your results. For the most part, I'm happy with the revised MS and also one of the initial reviewers is confident that the MS is now in shape for publication in BG. I have a few points that need clarification/modification (see below), before final publication.

Wit the best wishes, Helge Niemann

Abstract: remove paragraphs
P1, L1: define climatic intervals
P2, L5: acronym OM not defined

Intro
P3, L10: OM should refer to organic matter, not inorganic matter
P4, L7: use “these” instead of “their” (refs are in brackets, not mentioned specifically). Also use “also” instead of “as well” at the beginning of a sentence

Material and Methods
P4, L20. Usin “in the area” instead of “on the the area”
P4, L23. “dysoxic” is not really well defined term. <1µM O2? Rather use “microoxic” and give a definition. Also, if the water column is never stratified as indicated before (which I presume you didn’t intend), then low-O2 bottom water is somewhat strange (thoug the presence of anoxygenic phototrophs attests to reduced conditions. Thus, clarify the mixing regime of the lake, I guess it’s only the epilimnion and not the hypolymnion that mixes?
P4, L24. O2 penetration into sediments is usually very limited (µm to mm scale)
P5, L20. rephrase ”freshwater water column lake level highstand”

Results
P9, L15: acronym YD not explained
P10, L17: ratio of prokaryote/eukaryote not really clear. define.
P11, L8: erase “regardless”, it’s not clear which of the informations before are not taken into account

Discussion:
general:
- sometimes past tense is used, eg. P 14, L 18: sequences provided evidence. This needs to be changed to present tense: sequences PROVIDE evidence. Change accordingly
a more clear statement is needed to highlight that the distinction of ancient “fossilised” from modern is difficult
comparison to other stratified systems with bottom water anoxia (eg Lake Cadagno, Wirth et al., 2013) should be strengthened.
P13, L8: “position of the Westerlies moved to the site” not clear
P14/15, L32-3: This is textbook knowledge. Also, Methanomicrobiales can use substrates other than H2/CO2
P17, L17: it seems unlikely that isorenieratane is a diagenetic product arising from other pigments, particularly in light that you found okenone as well.

Figs: use µM or the like for concentrations