Benthic archaea as potential sources of tetraether membrane lipids in sediments across an oxygen minimum zone

Besseling, Marc A.; Hopmans, Ellen C.; Boschman, R. Christine; Sinninghe Damsté, Jaap S.; Villanueva, Laura

doi:https://doi.org/10.5194/bg-15-4047-2018

Articles | Volume 15, issue 13

https://doi.org/10.5194/bg-15-4047-2018

© Author(s) 2018. This work is distributed under
the Creative Commons Attribution 4.0 License.

https://doi.org/10.5194/bg-15-4047-2018

© Author(s) 2018. This work is distributed under
the Creative Commons Attribution 4.0 License.

Articles | Volume 15, issue 13

Research article

|

04 Jul 2018

Research article |

| 04 Jul 2018

Benthic archaea as potential sources of tetraether membrane lipids in sediments across an oxygen minimum zone

Marc A. Besseling, Ellen C. Hopmans, R. Christine Boschman, Jaap S. Sinninghe Damsté, and Laura Villanueva

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Final revised paper (published on 04 Jul 2018)
Supplement to the final revised paper
Preprint (discussion started on 19 Jul 2017)
Supplement to the preprint

Interactive discussion

Status: closed

AC: Author comment | RC: Referee comment | SC: Short comment | EC: Editor comment

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RC1: 'Review: Benthic Archaea as potential sources of tetraether membrane lipids in sediments across an oxygen minimum zone', Anonymous Referee #1, 30 Sep 2017
- AC1: 'Reply to reviewer 1', Marc Besseling, 13 Oct 2017
  - RC2: 'Reply to AC1', Anonymous Referee #1, 30 Nov 2017
    - AC2: 'Second reply to reviewer 1', Marc Besseling, 10 Jan 2018
RC3: 'Review of "Benthic Archaea as potential sources of tetraether membrane lipids in sediments across an oxygen minimum zone"', Julius S. Lipp, 11 Dec 2017
- AC3: 'Reply to reviewer 2', Marc Besseling, 15 Jan 2018

Peer-review completion

AR: Author's response | RR: Referee report | ED: Editor decision

ED: Reconsider after major revisions (23 Jan 2018) by Markus Kienast

AR by Marc Besseling on behalf of the Authors (23 Feb 2018)

ED: Referee Nomination & Report Request started (01 Mar 2018) by Markus Kienast

RR by Anonymous Referee #1 (12 Mar 2018)

Suggestions for revision or reasons for rejection

In their response letter, Besseling et al. did not respond to 16 of my initial comments (pertaining to lines 360-435 and Figure 1 of the original manuscript). Further, they should try to better implement some of the suggested changes to their manuscript, as detailed below.

Line 402-404: The authors need to include their assessment of ionization biases in the manuscript as this information is crucial for comparison with future studies: “We have assessed the difference between the HPLC-MS method using a diol-column used for the study here and the one that uses a reversed phase LC column (Wörmer et al., 2013) using a fresh sample of North Atlantic SPM. Looking at the ratio of MH:DH:HPH for cren and GDGT-0, the NP IPL method may underestimate the MH IPLs by a factor of 10. However, even when taking this into account, this does not change the conclusion of this study. We have focused our discussions on the HPH variety of the IPLs as this is the best life marker among the IPLs. MH-GDGTs are certainly produced directly by archaea but can also have a sizable fossil contribution and are decay products of DH- and HPH-GDGTs, especially in stored extracts. For the anoxic surface sediment at 885 mbsl we observed a discrepancy between the relative abundance of IPL derived CL-GDGT-0 and the IPL-GDGT-0 relative abundance reported in our manuscript. Even if our method underestimates the relative abundance of MHs, this discrepancy cannot be fully explained. We, therefore, remained this part in our discussion. However, we also highlight the fact that we underestimate the relative abundance of MHs in our study.”

Line 429-431: The authors changed their sentence but still omit the fact that the lipid type has previously been detected in marine sediments (Lipp and Hinrichs, 2009; Sturt et al., 2004) as pointed out by reviewer 2.

Line 121-125: As suggested by reviewer 2, the authors need to show the data of their comparison with the Lengger et al. (2012) paper in a supplementary table.

Other comments:
Supplement: I appreciate the addition of chromatograms to the supplement. For this to be of greater use to future applications of their method, the authors should add a base peak chromatogram showing the elution times of all quantified compounds relative to a standard.

Table 1: Explain abbreviations “BWO” “OPD” in caption.

Line 387-389: Any experimental evidence for the higher preservation potential?

Comments from the original review that need to be addressed (line numbers pertaining to original manuscript):

Line 360: Qin et al. did not study IPLs. A more appropriate reference would be Elling et al. (2017).

Line 360-363: I am quite confident that the predominance of HPH-GDGTs in the sediment is an artifact of the chromatographic method that results in severe underestimation of MH-GDGT (and potentially DH-GDGT) relative abundances. However, the notion that higher HPH-content relates to higher activity was also supported by culture studies (Elling et al., 2014).

Line 363: Neither Harvey et al. or Schouten et al. discuss HPH IPLs and do not provide any experimental evidence for degradation rates of HPH versus MH or DH or any other GDGT IPL types. Rephrase.

Line 369-371: Do you think these fossil IPLs extracellular or intracellular (Braun et al., 2016)? Is some of the DNA also fossil? Would the DNA be preserved differently (degradation rates) than the IPLs and how would this affect the interpretation of your results?

Line 372-373: How did the 0/crenarchaeol ratio change for the anoxic sites? If they change in a similar way, does that point to different sources of 0 versus crenarchaeol or to accumulation of fossil IPLs?

Line 380: Typo. “Acid hydrolysis”

Line 384-386: You should discuss here or elsewhere that some cultures exist from the Thermoplasmatales cluster, although most clades remain uncultivated. E.g. there are many (acidophilic, thermoacidophilic) Thermoplasmatales cultures for which lipids have been analysed and all of them produce GDGTs. Further, the recently cultivated Methanomassiliicoccales (closely related to the uncultivated TMEG group) have been shown to produce IPL-GDGTs such as MH-GDGT-0 (Becker et al., 2016). It is thus very likely that the rest of the uncultivated Thermoplasmatales-like archaea can produce GDGTs.

Line 388: The way these papers are referenced is highly misleading. Four of the five references do not relate to Woesearchaeota and the inference of Villanueva et al. (2017) that Woesearchaeota do not produce GDGTs is circumstantial at best without knowledge of the actual GDGT biosynthetic pathway. Rephrase.

Line 392-394: Becker et al. (2016) showed that BDGTs are detectable in a globally distributed set of marine sediments. It is therefore likely that these compounds would be present in your samples. I suspect that you would detect these compounds using different chromatographic conditions. Recently, Thermoplasma-related methanogens (Methanomassiliicoccales) have been identified as a source of BDGTs in the environment (Becker et al., 2016). Meador et al. (2015) also identified further phosphatidic and MH, DH-GDGTs in MCG-rich samples. Could the MCG be sources of these compounds in your samples?

Line 416: As stated earlier, DH-GDGT-0 isomers have been detected in Thaumarchaeota (Elling et al., 2014; Elling et al., 2015).

Line 422: Typo. “sediments”

Line 423: Also Elling et al. (2014).

Line 430: Please provide experimental evidence for the “recalcitrant nature of glycosidic bonds”.

Line 433-434: Again, very misleading references, as in Line 388. These works do not discuss the GDGT lipid biosynthetic pathway. Delete the sentence or rephrase.

Line 435: I disagree: Could you please specify how the source assignment of IPL-GDGTs has been improved?

Figure 1: It would be very helpful to have another set of two plots (surface, subsurface) next to A and B that shows summed IPLs by headgroup type or a synthesis of the data in Table 2.

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RR by Julius S. Lipp (25 Mar 2018)

Suggestions for revision or reasons for rejection

Re-review of “Benthic Archaea as potential sources of tetraether membrane lipids in sediments across an oxygen minimum zone” by Besseling et al.

I would like to thank the authors for adding more information about the analytical method regarding peak separation and the applied quantification method. It is now much easier to assess the results. Many of the previous analytical concerns have been alleviated by the newly introduced supplementary figures. Thank you also for the more balanced discussion of the stability of glycolipids and phospholipids and for addressing the other concerns of both reviewers.
However, my second main concern remains in the revised version, and I think the authors have missed the chance to clarify some of the discrepancies of the new data and the previous results (reviewer 2, general comment 2 and detailed comments 14). I do not understand the “good correspondence between the datasets when it comes to the DH and HPH IPLs” as this is not further explained. Instead, when comparing the relative ring distribution of Lengger et al. (2014) and the current study within each headgroup class, MH-GDGTs show the best resemblance, whereas DH- and HPH-GDGTs differ somewhat (see plots in attached PDF of Excel table). The lack of GDGT-0 in DH-GDGTs of sample 885 and 1306 and of HPH-GDGT in sample 885 in Besseling et al. is curious. Both studies used normal phase chromatography with diol column chemistry to separate the IPL-GDGT classes. If an unknown IPL-GDGT-0 is responsible for the observed GDGT-0 in the hydrolyzed DH- and HPH-GDGT fractions of Lengger et al. (2014) it would likely also elute in a similar retention time range on the diol column of Besseling et al. (between 19 and 35 min where DH- and HPH-GDGTs elute) and should therefore be visible in the chromatogram. Possibilities why the unknown IPL-GDGT-0 is not visible in the chromatogram are (a) they elute very early with the column void volume, (b) they elute very late and are retained on the column, and (c) the response of this compound is very low and they are “invisible” on the MS. Scenario (a) and (b) could be tested by reversed phase analysis to gain more insight into polarity ranges outside the optimal RT range for the diol column. Since the authors have access to RP chromatography as they state in the rebuttal letter this should not be too time consuming.
I agree that the differences in sampling resolution might explain some of the differences between the two studies. However, I would not expect a dramatic heterogeneity within 1.5 cm of sediment that could lead to the observed large differences. This explanation would require a 0-0.5cm layer almost devoid of GDGT-0 (to explain Besseling et al.) and an underlying 0.5-2cm layer loaded with GDGT-0 (to explain the integrated signal 0-2 cm in Lengger et al. 2014) which I find somewhat unlikely. Instead, Lengger et al. 2014 show similar GDGT distributions for the three studied surface sediment samples (0-2 cm depth), even within each IPL-class. These distributions also closely resemble GDGT distributions observed by direct analysis (without hydrolysis, similar to the Besseling et al. method) in pure cultures of thaumarchaea (e.g. Elling et al., 2014 GCA) which are abundant in the 885 sample (~30%, Fig. 1). What is the explanation for the 50% contribution of GDGT-2 in DH-GDGT of sample 3003? Can this unusual value be trusted?
My impression from the authors comments and the manuscript is that (a) MH abundance is problematic (perhaps up to factor 10 underestimated, this needs to be pointed out in the manuscript) and (b) IPL-GDGT-0 abundance is questionable for some headgroup classes. This implies that not all new data can be compared to the 2014 data which is unfortunate. Which dataset (2014 or the present one) is more credible? And which ring and IPL headgroup distribution should be referenced in future studies if the differences are so large?

Detailed comments
Line 106: delete “ppm“
Line 115: typo, “assess”
Line 121-123 and Line 213-216: I assume the reference should be Lengger et al. (2014)?
Line 294: “and, therefore, are likely”
Line 405: typo, “hydrolysis”. The sampling depth in Lengger et al. (2014) was different - 0-2 cm - as pointed out earlier.
Line 408: the underestimation of MH is mentioned in the rebuttal letter (reviewer 1, 2nd comments, 2) but is not included in the manuscript. This should be added to the method description or to the results. I do not agree with the authors’ statement to “retain a paragraph of discussion on this”. It is an important result necessary to judge the results.
Line 448: typo “sediments”
Table 2: check that numbers add up to 100% for each sample (e.g., sample 885-crenarchaeol: 1.3+43.1+0.3=46.7, also sum for sample 885=100.2%)

Referee Report: PDF

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ED: Reconsider after major revisions (11 Apr 2018) by Markus Kienast

AR by Marc Besseling on behalf of the Authors (02 May 2018) Author's response Manuscript

ED: Referee Nomination & Report Request started (07 May 2018) by Markus Kienast

RR by Anonymous Referee #1 (22 May 2018)

Suggestions for revision or reasons for rejection

Although the authors go to great length rebutting the comments of both reviewers, for most instances their reasoning is not reflected in the revised manuscript (in particular regarding the detailed technical explanations in the second report of reviewer 2). Although the manuscript would be acceptable for publication after minor revisions, I am taken aback by the authors’ reluctance to make meaningful changes to the text after three revisions. The review process should provide an opportunity for the authors to make their reasoning more accessible to the readers instead of trying to just brush off criticism. We want to understand your research and help make it more impactful. It is sad that the authors did not grasp this opportunity.

Line comments:

Line 347-357: I would suggest adding the recent paper by Yu et al. (2018, PNAS) to this discussion, which shows putative growth of group 8 MCG archaea on lignin and incorporation of bicarbonate into GDGTs.

Line 393: Please be precise on the details here and rephrase. Logemann et al. did not study GDGT degradation. It would be useful to discuss Xie et al. (2013, PNAS), who also studied archaeal glycolipids degradation. It is also not clear how the Logemann experiment would be relevant to the discussion of relative degradation rates of phospho- and glyco-GDGTs (or glyco vs. phosphor ether lipids), as they did not study this process.

Line 410-411: Please rephrase. After the last revision, it is no longer clear what “this discrepancy” refers to.

Line 414-417: Following our discussion in the review and rebuttal, rephrase “GDGT biosynthetic pathway” to “archaeal lipid biosynthetic pathway”, since only this statement is reasonably supported by the references. Alternatively, re-arrange the references to match each statement regarding lack of “archaeal lipid biosynthetic pathway (Jahn et al., 2004; Podar et al., 2013; Waters et al., 2003)” vs. “putatively lack the GDGT biosynthetic pathway (Villanueva et al., 2017)”

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ED: Publish subject to minor revisions (review by editor) (24 May 2018) by Markus Kienast

AR by Marc Besseling on behalf of the Authors (25 May 2018) Manuscript

ED: Publish subject to technical corrections (13 Jun 2018) by Markus Kienast

AR by Marc Besseling on behalf of the Authors (18 Jun 2018) Manuscript

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Short summary

Benthic archaea comprise a significant part of the total prokaryotic biomass in marine sediments. Here, we compared the archaeal diversity and intact polar lipid (IPL) composition in both surface and subsurface sediments with different oxygen regimes in the Arabian Sea oxygen minimum zone. The oxygenated sediments were dominated by Thaumarchaeota and IPL-GDGT-0. The anoxic sediment contained highly diverse archaeal communities and high relative abundances of IPL-GDGT-1 to -4.