the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
Archaeal lipostratigraphy of the Scotian Slope shallow sediments, Atlantic Canada
Abstract. The Scotian Slope in the North Atlantic Ocean extends ~500 km along the coast of Nova Scotia, Canada, descending from 400 m to 5 km water depth. With a maximum sediment thickness of ~24 km, large portions of the deeper basin are affected by salt tectonism, which has greatly impacted the basin stratigraphy and locally facilitated hydrocarbon seepage to the ocean seafloor. The surface sediments along the slope may therefore be home to microbial communities, which respond to complex geochemical drivers that not only include communication with the overlying water column, but also potential advection of deeper basinal fluids. Archaea are fundamental components of these communities, and their lipids act as important indicators of environmental conditions and microbial interactions within marine sediments. This study evaluates the spatial abundance and diversity of archaeal lipids preserved in shallow buried Scotian Slope sediments to better understand deep marine archaea community dynamics. Seventy-four sediment samples from 32 gravity and piston cores reaching a maximum depth of 9 meters below seafloor (mbsf) were collected during three survey cruises across a large region of the Scotian Slope. The survey area extends across ~40,000 km2, marking ~3° of latitudinal change over a water column depth that increases from ~1500 to 3500 m, of which one sampling site was a suspected cold seep environment. In total, 14 archaeal lipid classes comprising 42 unique compounds were detected. The lipid distributions reflect a high contribution of anaerobic methanotrophic (ANME) archaeal groups, such as ANME-1 to -3. Hierarchical cluster analysis (HCA) and principal components analysis (PCA) were used to show varying contributions of four lipid classes that included distinct assemblages of intact polar lipids (IPLs), which are largely sourced from living cells as well as core lipids (CLs), and their degradation products (CL-DPs) that collectively are sourced from different alteration stages following the death of the cell. From this, four stratigraphically distinct archaeal lipidomes, marking varying relative abundances of the lipid classes were observed in the upper 9 m of the surveyed slope sediments. One lipidome likely reflects archaeal communities impacted by a cold seep based on hydrocarbon head space gas analyses and high methane index and GDGT/Cren ratios. The other three lipidomes occur across overlapping sediment depth intervals in which the diversity and abundance of living, fossil, and degraded core lipids systematically change in what is likely depth. These changes likely mark systematic geochemically controlled, microbial community variations that are accompanying an increasing stockpile of diagenetic altered CLs. The three ambient sediment lipidomes appear to be highly conserved across the latitudinal extent of the study area marking a resolvable shallow sediment lipostratigraphy for the Scotian Slope.
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RC1: 'Comment on egusphere-2025-1228', Anonymous Referee #1, 06 May 2025
Please refer to the attached PDF for my review of your manuscript.
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AC1: 'Reply on RC1', G Todd Ventura, 28 May 2025
We greatly appreciate the careful and detailed review of our paper and do not have any comments to contest the list of required edits required to amend the text, tables, and figures as outlined. We would also like to say that the revision will take on additional changes as expressed in Reviewer 2’s comments. To the latter issue, we have been in contact with the editor about adding figures and amending the paper’s text to better express the complexity of the sedimentary environment. The changes do not impact the spatial relationships of the resolved lipostratigraphy. They do, however, impact the sourcing of the lipids and diagenetic alteration of various lipid classes.
Citation: https://doi.org/10.5194/egusphere-2025-1228-AC1 -
AC2: 'Reply on RC2', G Todd Ventura, 28 May 2025
The comment was uploaded in the form of a supplement: https://egusphere.copernicus.org/preprints/2025/egusphere-2025-1228/egusphere-2025-1228-AC2-supplement.pdf
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AC1: 'Reply on RC1', G Todd Ventura, 28 May 2025
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RC2: 'Comment on egusphere-2025-1228', Anonymous Referee #2, 08 May 2025
In the manuscript “Archaeal lipostratigraphy of the Scotian Slope shallow sediments, Atlantic Canada” Ahangarian et al. present the archaeal lipidomes in a wide range of sediments taken across the Scotian Slope. I was impressed by the large dataset which covers such a broad geographical range. I am generally accepting of the methods utilized and the lipid data itself looks interesting and valid. However, my concern about the manuscript is in the interpretation and discussion of the data. I feel that authors have not sufficiently reviewed the literature on archaea and archaeal lipids, which in turn has had a considerable effect on how they interpret their data.
One major issue is that the authors have made the assumption that glycosidic GDGTs are indicative of living archaea. This has been shown extensively to not be true, both experimentally and in the environment. Glycosidic GDGTs are known to be preserved for thousands and even millions of years. GDGTs with phospho-bound head groups are more accurate markers of living or recently living cells. However, the authors do not detect phospho-bound GDGTs, only some phospho-bound archaeols. The authors have failed to correctly interpret some of the literature they cite, such as the review of Schouten et al. (2013) which clearly states that “these IPLs may be of fossil origin, as degradation of ether lipids with a sugar head group, or even IPL GDGTs in general can proceed much more slowly than that of regular bacterial ester-bound IPLs.”. I draw the authors’ attention to more recent work that also shows that glycosidic IPL GDGTs cannot be used as markers for living archaea (Wu et al., 2019) and ask that the reviewers read this and the literature cited in its introduction. As a result of this error, amongst others listed below, the authors should go back and fully rewrite their manuscript to take this into account, carefully reexamining their assertions from their data about “living, fossil and degraded lipids”. Indeed, it would seem possible (or even probable) that the vast majority of the GDGTs detected originate from the overlying water column, not from the sediment itself. This is going to have considerable effect on the manuscript and hence I suggest major revisions to accomplish this.
Overall, I find it quite risky that the authors using the profiles of the photosynthetic pigment chl-a and its alteration product OH-chl-a in order to interpret the lipid data. The lipid extraction method used is not designed for pigment extraction, nor is the analysis method. As this pigment is notoriously easy to destroy with light, heat or acid, there is a risk that the depth profile of these compounds is an effect of variable extraction efficiency. The authors need to examine experimentally how rigorous their extraction methodology is for chlorophyll. As I stated above, OH-chl-a is an alteration product of chl-a (often formed during extraction), so I would not describe it as a photosynthetic pigment (Steele et al., 2018).
Another issue in terms of the authors’ interpretation of the literature, is the assignment of GDDs as GDGT degradation products. This is indeed the conclusion of Hingley et al. (2024), however the other article cited, (Mitrović et al., 2023), makes a quite different statement “it seems unlikely that GDDs are a direct diagenetic product of GDGTs. Overall, the observations from our study support the theory of a joint cellular origin for GDGTs and GDDs.”. It is ok if the authors of this manuscript to not agree with Mitrović et al. (2023), but they should not incorrectly present the conclusions of that study.
The authors also need to address the language used throughout. During revision this manuscript should be carefully read through and checked. As I have asked for major revisions, I will not do a line-by-line list of edits, as so much is likely to change. However here are some edits I would draw to the authors' attention.
Writing general – when rewriting this should be tightened up with fewer words and sharper sentences.
Line 21 and in more places throughout the manuscript (e.g. line 64). It’s not clear here what the authors mean here by deep. Is that deep sea or deep sediment.
Line 53. Thaumarchaeota were reclassed a few years ago as Nitrososphaerota (Rinke et al., 2021). I’m not suggesting that you use this newer term throughout the manuscript, but it should be mentioned here.
Line 74. I think you should redefine all abbreviations in the introduction and not rely on them being defined in the abstract.– e.g. IPL and CL
Table 1 – this needs to be improved visually and a lot of the information (such as sediment extracted and TLE weight) moved to a supplementary table.
Figure 1 (and others) – seems very fuzzy.
Line 236. This isomer of crenarchaeol is not a regioisomer and is hence no longer called this (cf. Sinninghe Damsté et al., 2018). Please read the up-to-date literature on this subject.
Entire section 4.1. Many of lines read poorly and should be rewritten for clarity. Additionally, the authors emit some significant recent work on the GDGTs of Thaumarchaeota, e.g. Elling et al. (2017) and Bale et al. (2019) and on hydroxy GDGTs e.g. (Varma et al., 2024).
Articles mentioned in the review
Bale, N.J., Palatinszky, M., Rijpstra, W.I.C., Herbold, C.W., Wagner, M., Sinninghe Damsté, J.S., 2019. Membrane Lipid Composition of the Moderately Thermophilic Ammonia-Oxidizing Archaeon “Candidatus Nitrosotenuis uzonensis” at Different Growth Temperatures. Applied and Environmental Microbiology 85. doi:10.1128/AEM.01332-19
Elling, F.J., Könneke, M., Nicol, G.W., Stieglmeier, M., Bayer, B., Spieck, E., de la Torre, J.R., Becker, K.W., Thomm, M., Prosser, J.I., Herndl, G.J., Schleper, C., Hinrichs, K.-U., 2017. Chemotaxonomic characterisation of the thaumarchaeal lipidome. Environmental Microbiology 19, 2681–2700.
Hingley, J.S., Martins, C.C., Walker-Trivett, C., Adams, J.K., Naeher, S., Häggi, C., Feakins, S.J., Naafs, B.D.A., 2024. The global distribution of Isoprenoidal Glycerol Dialkyl Diethers (isoGDDs) is consistent with a predominant degradation origin. Organic Geochemistry 192, 104782.
Mitrović, D., Hopmans, E.C., Bale, N.J., Richter, N., Amaral-Zettler, L.A., Baxter, A.J., Peterse, F., Miguel Raposeiro, P., Gonçalves, V., Cristina Costa, A., Schouten, S., 2023. Isoprenoidal GDGTs and GDDs associated with anoxic lacustrine environments. Organic Geochemistry 178, 104582.
Rinke, C., Chuvochina, M., Mussig, A.J., Chaumeil, P.-A., Davín, A.A., Waite, D.W., Whitman, W.B., Parks, D.H., Hugenholtz, P., 2021. A standardized archaeal taxonomy for the Genome Taxonomy Database. Nature Microbiology 6, 946–959.
Schouten, S., Hopmans, E.C., Sinninghe Damsté, J.S., 2013. The organic geochemistry of glycerol dialkyl glycerol tetraether lipids: A review. Organic Geochemistry 54, 19–61.
Sinninghe Damsté, J.S., Rijpstra, W.I.C., Hopmans, E.C., den Uijl, M.J., Weijers, J.W.H., Schouten, S., 2018. The enigmatic structure of the crenarchaeol isomer. Organic Geochemistry 124, 22–28.
Steele, D.J., Kimmance, S.A., Franklin, D.J., Airs, R.L., 2018. Occurrence of chlorophyll allomers during virus-induced mortality and population decline in the ubiquitous picoeukaryote Ostreococcus tauri. Environmental Microbiology 20, 588–601.
Varma, D., Villanueva, L., Bale, N.J., Offre, P., Reichart, G.-J., Schouten, S., 2024. Controls on the composition of hydroxylated isoprenoidal glycerol dialkyl glycerol tetraethers (isoGDGTs) in cultivated ammonia-oxidizing Thaumarchaeota. Biogeosciences 21, 4875–4888.
Wu, W., Xu, Y., Hou, S., Dong, L., Liu, H., Wang, H., Liu, W., Zhang, C., 2019. Origin and preservation of archaeal intact polar tetraether lipids in deeply buried sediments from the South China Sea. Deep Sea Research Part I: Oceanographic Research Papers 152, 103107.
Citation: https://doi.org/10.5194/egusphere-2025-1228-RC2 -
AC2: 'Reply on RC2', G Todd Ventura, 28 May 2025
The comment was uploaded in the form of a supplement: https://egusphere.copernicus.org/preprints/2025/egusphere-2025-1228/egusphere-2025-1228-AC2-supplement.pdf
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AC1: 'Reply on RC1', G Todd Ventura, 28 May 2025
We greatly appreciate the careful and detailed review of our paper and do not have any comments to contest the list of required edits required to amend the text, tables, and figures as outlined. We would also like to say that the revision will take on additional changes as expressed in Reviewer 2’s comments. To the latter issue, we have been in contact with the editor about adding figures and amending the paper’s text to better express the complexity of the sedimentary environment. The changes do not impact the spatial relationships of the resolved lipostratigraphy. They do, however, impact the sourcing of the lipids and diagenetic alteration of various lipid classes.
Citation: https://doi.org/10.5194/egusphere-2025-1228-AC1
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AC2: 'Reply on RC2', G Todd Ventura, 28 May 2025
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