Bijl and co-authors present a comprehensive review of GDGTs, with focus on marine isoprenoid GDGTs, and their consensus on best practices for sampling, processing, analyses, interpretation, and archiving. This is an impressive effort that transcends the typical review focused on research-focused questions. I greatly appreciated the detailed compilation of sample prep, processing and analytical considerations, which will be useful to anyone new to the field or simply in need of a handy reference in their lab. The archiving section is also timely given the more recent shift to open science and big data synthesis efforts. Following some minor revisions and considerations, I think this paper will be a valuable addition to the GDGT (and biomarker) literature.

--David Harning

General: Structure could be improved in places. Sometimes paragraphs are really short and others overly long. To improve flow in a monster paper like this, it is important to try to stick with topic and concluding sentences for paragraphs to enhance the flow and readability for the reader.

Title: While GDGTs are most often used to reconstruction temperature, as authors note in the text, other environmental factors are known to influence their distributions. Recently, it has been exciting to see efforts to use GDGT distributions to reconstruct these other processes (e.g., archaeal ecology, nutrients, etc.). Hence, I may suggest that “paleotemperatures” is changed to “paleoenvironments”. Or somehow recognize these other factors. Otherwise, I feel the authors are pigeonholing this proxy into just temperature, which we know is rarely the only factor.

Specific points:

L103-104: Change to’s to with’s

L111: I suggest a new paragraph here on brGDGTs. Bump the first sentence on isoGDGTs to the next paragraph where those compounds are being discussed.

L121-130: This paragraph on GDGTs could use some reference to the other factors that may influence their distribution besides temperature, as discussed in detail later in the text. Having this upfront will hopefully ensure GDGT users remain cautious with temperature interpretations.

L131: The final sentence on OH-GDGTs could become its own new paragraph with a similar level of discussion on environmental considerations as given to the branched and isoprenoid GDGTs before.

L139: I would suggest given the uncertainties around what temperature or water depth GDGTs may capture, you leave it as past ocean temperature rather than sea surface temperature

L142: remove and

Figure 1: Only because they are my own, I noticed that Baffin Bay core top samples are not included in the map (Harning et al., 2023). Please make sure that any other sites that may be missing are included as well.

L162: Instead of “right kind”, perhaps change to needed. Right kind sort of implies there is a wrong kind or bad type of data, which I don’t think is the intent

L163: The PhanSST example is given but another sentence could be added to better demonstrate how this example serves the authors point

L164: remove greatly – it’s too relative of a term and doesn’t mean much

L165-166: I agree this is important and as I note at the end, perhaps foreshadowing some next steps would be helpful. May not be needed here in the introduction though. I suggest maybe in lieu of conclusions at the end – see final comment

L168-176: This list appears abruptly and seems out of place. If you wish to keep, it needs some intro text. I think it could be removed though.

L187: change this to these

L188: subsurface “sediment”? Also please clarify what shallow means if there are any numbers

L201: remove really

L208: How do we know when the outcrop sediment is not affected by weather? How deep do we need to excavate to ensure samples are optimal?

L226: Instead of sea above, simply reiterate the temperature threshold again for the reader

L233: Regarding coring contamination, it’s also important to note that we do this as the core tubing itself is often some form of plastic that should be avoided for potential contamination too. Also important to consider because the internal sediments are least deformed by coring

L239: I think you’re missing the age here; the outcrop is modern right?

L251: SIM is not always used

L258-260: Most of this seems better placed with the sample processing overview. Maybe just keep ones relevant for field and sub-sampling? Same for following paragraph

L303: Our lab does 2x, I see 3x a lot, but based on our analyses, the majority (sorry I don’t have numbers in front of me) is extracted with 2. Including either of both numbers seem helpful here. Also, might be worth noting that cleaning the ASE with pure methanol (or some other polar solvent) rinses between batches is helpful to avoid cross-contamination

L356: IPL extractions could be its own section, so it’s not lost in here with ultrasonic

L369: This paragraph seems applicable to all extraction methods so maybe not include under ultrasonic. May also be worth noting to not dry down to completion under N2 gas to avoid losing more volatile compounds

L394: I think this paragraph should be joined with the previous

L412: remove there

L487: not always, we use full scan with an orbitrap and then extract ion chromatograms

Figure 2: This is really cool data to see!

L673: This isoGDGT-0/cren value of 2, based on my understanding, is completely arbitrary and I’m not convinced we have a good threshold for this ratio and how it relates to dominant GDGT producers. Culture experiments would help. Would be good to articulate if similar for other thresholds discussed in this review.

Table 2: Some equations are cut off. Also please provide references for status column recommendations if not already included.

L908: This is an example of a paragraph that lacks appropriate structure with e.g., topic sentences. It is rather long and could be revised to improve clarity.

L927: What is the “GDGT review paper”? Reference?

Table 3: Some equations are cut off

L1089: Remove very - it’s too relative of a term and doesn’t mean much

L1120: World Data “Service” if you are referring to NOAA

L1243: The conclusions are quite brief, which is maybe okay given the details included in the manuscript and that this is a review. That being said, I miss some sort of synopsis on what the possible next steps may be. This could be included here instead of conclusions. How do we ensure community buy-in and the incorporation of the entire GDGT community? I understand this review came out of the GDGT workshop, but many folks, including myself, could not attend due to cost, distance, etc. How do we make this more inclusive for people from outside Europe, who were the main attendees for the workshop, and from other often less represented regions of the globe (e.g., global south)? In this sense, I would not say this represents a “large” part of the lipid biomarker community. For next steps, virtual workshops seem like a good opportunity and perhaps some sort of GDGT-specific database that incorporates the metadata fields highlighted in the final section. Just some things to think about that might help this review helpful in implementing the key take-aways from this paper.

The work by Bijl et al. presents an overview of the state of the art of the analysis and interpretation of GDGTs in the marine environment. In this review the authors discuss the processing of GDGT related information from the sample collection, analysis, to ultimately the long-term storage of the information for future use, following the FAIR principles. Along the text the authors discuss both the history, current state, as well as considerations for each of the steps. I find the review very engaging and easy to read, with the structure of the text accessible for people that might want to consult specific details on the topic.

I am happy to recommend this manuscript for publication once some minor comments are addressed.

Line 107. Change "Next to these". Additionally, the list of compounds in this paragraph breaks the flow of the idea. Consider breaking the paragraph.

Line 110 (and others). My recommendation would be to stick with "GMGTs" as that's the most descriptive name. For clarity I understand making the clarification, but later they should be referred as GMGTs.

Lines 139. I am not sure if IPLs are mentioned enough in the rest of the text to include them in this sentence.

Line 258. Correct this section: "all metal tools.extraction"

Section 3.2. This section would benefit from some references.

Line 329. I don't know if I would make emphasis on Soxhlet being used for "larger samples" when the described range is very close to that of ASE.

Line 345. Consider starting a new section or starting a new paragraph here.

Line 348. Here the Bligh-Dyer method is mentioned but only a very brief description is given, and it is not until a paragraph later that some information about this protocol is given. Maybe it would be worth explaining it within the Ultrasonic extraction section.

Line 373. Make the 2 underscore in N2.

Lines 547-548. I am not sure why the temperatures are given in F here.

Line 576. I think this should be Figure 3f?

Section 6.7. Maybe the explanation of how OPTiMAL could be improved, since it is a bit hard to follow.