the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
| 17 Jun 2024
Controls on the composition of hydroxylated isoGDGTs in cultivated ammonia oxidizing Thaumarchaeota
Abstract. Membrane lipids of ammonia-oxidizing Thaumarchaeota, in particular isoprenoidal glycerol dialkyl glycerol tetraethers (isoGDGTs) and hydroxylated isoGDGTs (OH-isoGDGTs), have been used as biomarkers and as proxies in various environments. Controlled growth experiments have been used to investigate the factors that influence the composition of these lipids, in particular on how these factors affect the TEX86 temperature proxy, which is based on the degree of cyclization of isoGDGTs. Recently, the ring index of OH-isoGDGTs (RI-OH'), based on cyclization patterns of OH-isoGDGTs, and the relative abundance of OH-isoGDGTs (%OH) have emerged as promising temperature proxies. Here, we examined the impact of growth temperature and growth phase on the distribution of OH-isoGDGTs and their associated proxies using cultures of two thaumarchaeotal strains. Analysis of core lipids and headgroup compositions of isoGDGTs and OH-isoGDGTs showed no consistent differences between the mid-exponential and stationary phases for both strains. Nitrosopumilus adriaticus NF5 shows a substantially higher relative abundance of OH-isoGDGTs (~49 %) compared to Nitrosopumilus piranensis D3C (~5 %) and also relative to observations reported for core lipids in the marine environment (< 17 %), indicating large variations in %OH values even among closely related species. Unlike in the marine environment, the %OH did not decrease with increasing temperatures in either of the strains, possibly reflecting a threshold below 15 °C for this response in natural environment. The RI-OH' increases with increasing temperature in cultures of both strains, similar to the ring index of regular isoGDGTs. The relative abundances of the headgroups varied between strains and did not respond to changes in temperature nor growth phase. The %OH and RI-OH' calculated from intact polar lipids with different headgroups revealed large differences between the distinct intact polar lipids, similar to that previously observed for regular isoGDGTs. Together, our findings suggest that growth temperature has a pronounced effect on the degree of cyclization in isoGDGTs and OH-isoGDGTs, in contrast to the relative abundance of OH-isoGDGTs, which mainly exhibits interspecies variability.
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Notice on discussion status
The requested preprint has a corresponding peer-reviewed final revised paper. You are encouraged to refer to the final revised version.
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Preprint
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Supplement
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The requested preprint has a corresponding peer-reviewed final revised paper. You are encouraged to refer to the final revised version.
- Preprint
(1159 KB) - Metadata XML
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Supplement
(666 KB) - BibTeX
- EndNote
- Final revised paper
Journal article(s) based on this preprint
Interactive discussion
Status: closed
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RC1: 'Comment on egusphere-2024-1773', Anonymous Referee #1, 26 Jul 2024
This manuscript uses cultures of two Thaumarchaeotal strains to investigate growth temperature and phase on OH-GDGT distributions and OH-GDGT-based proxies. This is an important piece of work in the context of the emergence of OH-GDGTs as a GDGT-based temperature indicator, especially in cold water settings. The paper is clear and well written with nicely presented figures, and thoroughly reported results. I mostly only have a few very minor suggested comments/changes, but did feel like the manuscript was missing an ‘implications’ or ‘summary’ section to tie the results together and put them into a wider context. Could the authors comment on what they see as the key implications of interspecies variability in OH-GDGTS with changes in growth temperature for OH-GDGT-based temperature proxies? Specific comments below:
Line 23. Add ‘the’ before natural.
Line 32. Add a comma between ‘moieties’ and ‘and’.
Line 43. Add ‘the’ before Black Sea.
Line 141. Correct format for tex86oh.
Figure 3: Is there a reason purple shaded boxes haven’t been added to c) and g)? It would be good to see how these results compare to global core top data sets for RI isoGDGTs.
Line 347: Extent rather than extend.
Discussion: It feels like an implications section is missing here, that sums up the results and discussion and distills out the key points and implications of these findings for future OH-GDGT- based research. I recommend adding a paragraph to this effect before the conclusions.
Citation: https://doi.org/10.5194/egusphere-2024-1773-RC1 - AC1: 'Reply on RC1', Devika Varma, 23 Aug 2024
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RC2: 'Comment on egusphere-2024-1773', Anonymous Referee #2, 25 Aug 2024
This manuscript systematically investigates the response of hydroxylated GDGTs (OH-GDGTs) in ammonia-oxidizing archaea to temperature variations and different growth phases, revealing several significant findings. The manuscript is well-written, the data are presented clearly, and the conclusions are substantial and scientifically meaningful. However, I have two main concerns and a few suggestions for further research:
1. The study uses the Bligh-Dyer method for lipid extraction, and it is mentioned that this method may lead to partial dehydration of hydroxylated isoGDGTs, potentially underestimating the abundance of OH-isoGDGTs. This could partly explain the discrepancies observed between experimental data and environmental samples. I recommend that the authors discuss the potential impact of this extraction method on the results more thoroughly and consider whether alternative extraction methods might more accurately reflect the GDGT composition in pure cultures. I would recommend considering the use of cellular acid hydrolysis in future studies to investigate the response of core lipids systematically in the future. This approach may provide a more comprehensive understanding of how core lipids behave under different conditions and could help to address some of the limitations observed with the current extraction methods.
2. Figure 1 shows that the N. piranensis D3C strain exhibits some differences at higher temperatures, particularly at 35°C, where the relative abundance of OH-isoGDGTs differs significantly between growth phases. However, the discussion of this aspect in the manuscript is somewhat brief. I suggest the authors provide a more detailed explanation of the mechanisms by which high temperatures might influence these differences, especially when compared with environmental observations.
3. Given that the study found inconsistencies between the behavior of OH-GDGTs in the experimental setting and in environmental samples, particularly regarding temperature's effect on cyclization but limited impact on OH%, future research could focus on the performance of different strains at lower temperatures (<15°C), especially those isolated from cold/polar regions. This could provide valuable insights into the physiological role of OH-GDGTs in archaeal membrane adaptation and further refine the proxies based on them.
I believe that this manuscript makes a significant contribution to our understanding of OH-GDGT proxies and is worthy of publication.Â
Citation: https://doi.org/10.5194/egusphere-2024-1773-RC2 - AC2: 'Reply on RC2', Devika Varma, 28 Aug 2024
Interactive discussion
Status: closed
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RC1: 'Comment on egusphere-2024-1773', Anonymous Referee #1, 26 Jul 2024
This manuscript uses cultures of two Thaumarchaeotal strains to investigate growth temperature and phase on OH-GDGT distributions and OH-GDGT-based proxies. This is an important piece of work in the context of the emergence of OH-GDGTs as a GDGT-based temperature indicator, especially in cold water settings. The paper is clear and well written with nicely presented figures, and thoroughly reported results. I mostly only have a few very minor suggested comments/changes, but did feel like the manuscript was missing an ‘implications’ or ‘summary’ section to tie the results together and put them into a wider context. Could the authors comment on what they see as the key implications of interspecies variability in OH-GDGTS with changes in growth temperature for OH-GDGT-based temperature proxies? Specific comments below:
Line 23. Add ‘the’ before natural.
Line 32. Add a comma between ‘moieties’ and ‘and’.
Line 43. Add ‘the’ before Black Sea.
Line 141. Correct format for tex86oh.
Figure 3: Is there a reason purple shaded boxes haven’t been added to c) and g)? It would be good to see how these results compare to global core top data sets for RI isoGDGTs.
Line 347: Extent rather than extend.
Discussion: It feels like an implications section is missing here, that sums up the results and discussion and distills out the key points and implications of these findings for future OH-GDGT- based research. I recommend adding a paragraph to this effect before the conclusions.
Citation: https://doi.org/10.5194/egusphere-2024-1773-RC1 - AC1: 'Reply on RC1', Devika Varma, 23 Aug 2024
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RC2: 'Comment on egusphere-2024-1773', Anonymous Referee #2, 25 Aug 2024
This manuscript systematically investigates the response of hydroxylated GDGTs (OH-GDGTs) in ammonia-oxidizing archaea to temperature variations and different growth phases, revealing several significant findings. The manuscript is well-written, the data are presented clearly, and the conclusions are substantial and scientifically meaningful. However, I have two main concerns and a few suggestions for further research:
1. The study uses the Bligh-Dyer method for lipid extraction, and it is mentioned that this method may lead to partial dehydration of hydroxylated isoGDGTs, potentially underestimating the abundance of OH-isoGDGTs. This could partly explain the discrepancies observed between experimental data and environmental samples. I recommend that the authors discuss the potential impact of this extraction method on the results more thoroughly and consider whether alternative extraction methods might more accurately reflect the GDGT composition in pure cultures. I would recommend considering the use of cellular acid hydrolysis in future studies to investigate the response of core lipids systematically in the future. This approach may provide a more comprehensive understanding of how core lipids behave under different conditions and could help to address some of the limitations observed with the current extraction methods.
2. Figure 1 shows that the N. piranensis D3C strain exhibits some differences at higher temperatures, particularly at 35°C, where the relative abundance of OH-isoGDGTs differs significantly between growth phases. However, the discussion of this aspect in the manuscript is somewhat brief. I suggest the authors provide a more detailed explanation of the mechanisms by which high temperatures might influence these differences, especially when compared with environmental observations.
3. Given that the study found inconsistencies between the behavior of OH-GDGTs in the experimental setting and in environmental samples, particularly regarding temperature's effect on cyclization but limited impact on OH%, future research could focus on the performance of different strains at lower temperatures (<15°C), especially those isolated from cold/polar regions. This could provide valuable insights into the physiological role of OH-GDGTs in archaeal membrane adaptation and further refine the proxies based on them.
I believe that this manuscript makes a significant contribution to our understanding of OH-GDGT proxies and is worthy of publication.Â
Citation: https://doi.org/10.5194/egusphere-2024-1773-RC2 - AC2: 'Reply on RC2', Devika Varma, 28 Aug 2024
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Laura Villanueva
Nicole Bale
Pierre Offre
Gert-Jan Reichart
Stefan Schouten
The requested preprint has a corresponding peer-reviewed final revised paper. You are encouraged to refer to the final revised version.
- Preprint
(1159 KB) - Metadata XML
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Supplement
(666 KB) - BibTeX
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- Final revised paper