Hydrothermal inputs drive dynamic shifts in microbial communities in Lake Magadi, Kenya Rift Valley

Collins, Evan R.; Ferland, Troy M.; Castañeda, Isla S.; Owen, R. Bernhart; Lowenstein, Tim K.; Cohen, Andrew S.; Renaut, Robin W.; O'Beirne, Molly D.; Werne, Josef P.

doi:https://doi.org/10.5194/egusphere-2024-3006

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https://doi.org/10.5194/egusphere-2024-3006

Preprints

02 Oct 2024

| 02 Oct 2024

Hydrothermal inputs drive dynamic shifts in microbial communities in Lake Magadi, Kenya Rift Valley

Evan R. Collins, Troy M. Ferland, Isla S. Castañeda, R. Bernhart Owen, Tim K. Lowenstein, Andrew S. Cohen, Robin W. Renaut, Molly D. O'Beirne, and Josef P. Werne

Abstract. The Methane Index (MI) is an organic geochemical index that uses isoprenoid glycerol dialkyl glycerol tetraethers (GDGTs) as a proxy for methane cycling. Here, we report results from core spanning > 700 ka in Lake Magadi, Kenya, which shows abrupt shifts between high and low MI values in the core. These shifts coincide with interbedded tuffaceous silt. Where tuffaceous silts are present, MI “switches off” (MI < 0.2); in contrast, where these silts are absent in the core, the MI increases (MI > 0.5). Bulk organic matter is enriched in ¹³C in Magadi during “MI-off” periods, with values of ~ −18 ‰ in the upper part of the core and −22 to −25 ‰ in the lower portion. Evidence from n-alkanes and fatty acid methyl esters (FAMEs) support previous interpretations of an arid environment with a shallower lake where Thermoproteotal (formerly Crenarchaeota) archaea thrive in a hot spring rich environment over Euryarchaeota. Sediments deposited when the MI switches “on” showed δ¹³C_OM values as low as −89.4 ‰, but most were within the range of −28 to −30 ‰, which is consistent with contributions from methanogens rather than methanotrophs. Thus, the likely source of these high MI values in Lake Magadi is methanogenic archaea. Our results show that hydrothermal inputs of bicarbonate-rich waters into Lake Magadi cause a shift in the dominant archaeal communities, alternating between two stable states.

Received: 25 Sep 2024 – Discussion started: 02 Oct 2024

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14 Aug 2025

Hot-spring inputs and climate drive dynamic shifts in archaeal communities in Lake Magadi, Kenya Rift Valley

Evan R. Collins, Troy M. Ferland, Isla S. Castañeda, R. Bernhart Owen, Tim K. Lowenstein, Andrew S. Cohen, Robin W. Renaut, Molly D. O'Beirne, and Josef P. Werne

Biogeosciences, 22, 3931–3948, https://doi.org/10.5194/bg-22-3931-2025,https://doi.org/10.5194/bg-22-3931-2025, 2025

Short summary

Evan R. Collins, Troy M. Ferland, Isla S. Castañeda, R. Bernhart Owen, Tim K. Lowenstein, Andrew S. Cohen, Robin W. Renaut, Molly D. O'Beirne, and Josef P. Werne

Interactive discussion

Status: closed

RC1:
'Comment on egusphere-2024-3006', Anonymous Referee #1, 23 Oct 2024

Please see the attached document.

Citation: https://doi.org/10.5194/egusphere-2024-3006-RC1
- AC1: 'Reply on RC1', Evan Collins, 27 Jan 2025
  
  Hello, please see the attached PDF file for Referee #1.
  
  Citation: https://doi.org/10.5194/egusphere-2024-3006-AC1
RC2:
'Review egusphere-2024-3006', Anonymous Referee #2, 05 Nov 2024
The authors investigated sections of a drill core from Lake Magadi (Hominin Sites and Paleolakes Drilling Project, HSPDP), a soda lake in Kenya, to reconstruct the microbial methane cycle of the lake system over the last 456 ka. The study is focused on molecular biomarker analysis, especially isoGDGTs, representing archaeal core lipids. Together with accompanying (organic-) geochemical data and published information, the authors interpret periodical shifts in microbial methane cycling (and consequently the archaeal community) to be associated with changes in the hydrothermal input at Lake Magadi. It is indicated that phases of low hydrothermal activity show increased microbial methane cycling as compared to phases of high hydrothermal activity.
Soda lakes are important habitats for life. Their investigation, including the microbial methane cycle over time, provides valuable information on these extreme environments and potential early Earth habitats. A detailed reconstruction of the microbial methane cycle of Lake Magadi over time does not exist so far. The findings of the study by Collins et al. are new, complement existing data, and improve our understanding of the Magadi system. The used core samples from the HSPDP are unique, and represent excellent material to study archaeal communities/the microbial methane cycle of Lake Magadi over time. However, the manuscript needs to be substantially improved in some areas before publication:
(i) The sampling strategy is not optimal (cf., l. 129–133). The authors focused on samples that were expected to have high total organic carbon contents (data not presented in the manuscript), which was only assessed by visual inspection (dark brown to black silty clay). The authors argue that those samples would yield the best results. This may have created a biased data set (also samples with low organic carbon contents may show a great molecular diversity). Additionally, the sampling scheme is not consistent. Between the defined intervals #1–6, several meters of core are not covered (3–15 m between single intervals), while within an interval the sampling steps are in parts as close as a few centimeters. It would be interesting to see, if microbial methane cycling was also active during the deposition of sediments with low organic carbon content.
(ii) The study lacks bulk geochemical data of the samples, which would be important to contextualize the presented biomarker and isotope data (e.g., total organic and inorganic carbon carbon contents, total sulfur content, bulk ¹³C_carb). Especially stable carbon isotope data of the carbonate phase (δ¹³C_carb) would improve the discussion of shifts in methane cycling (it seems that at least some samples contain carbonate, as the samples were acid-leached before ¹³C_org analysis; l. 174–175).
(iii) The presented bulk δ¹³C_org data lack context. In lake systems primary production and/or terrestrial input usually govern the carbon cycle. The presented data do not allow the assessment of the role of microbial methane cycling in the lake’s carbon cycle over time. It would help to present total abundances of compounds in relation to the total organic carbon content (amount per g TOC). In addition, the ¹³C_org data should be discussed together with the leaf wax data to evaluate the influence of terrestrial input on the ¹³C_org values. In the presented data set, only three values in interval #2 indicate methanotrophy (−48.1‰, −64.2‰, −89.4‰; Table 1), the rest of the ¹³C_org values could also be explained by variations in primary production and/or terrestrial input.
(iv) The discussion of microbial sulfate reduction in the system (e.g., l. 366–379) is not based on a solid data set. In the current version, only C_17:0 FAME and the appearance of pyrite are used to track microbial sulfate reduction. The C_17:0 FAME, however, is not only produced by sulfate reducers and represents a weak biomarker. Furthermore, it seems that only few samples contain C_17:0 FAME, and it does not necessarily co-occur with pyrite (cf., Table 1). The authors also speculate on the sulfate availability without presenting any robust indication on sulfate levels. Without further data (e.g., sulfur content, stable sulfur isotope composition of the pyrites) this part of the discussion needs to be significantly reduced.
(v) The interpretation of increased microbial methane cycling at times of low hydrothermal input (and vice versa) is mainly based on the correlation of MI with REE data and Ca/Na-ratio. These data sets, however, do not always match (cf., figure 4). The authors should discuss the discrepancies in more detail, and present some explanations for the major discrepancies (e.g., low Ca/Na at the end of interval #2, high Ca/Na together with low REE abundance in interval #5, high REE abundance together with low Ca/Na at the end of interval #6). The MI data set seems to be much more consistent.

More specific comments:
The title is misleading, as the manuscript is focusing on the reconstruction of the microbial methane cycle in Lake Magadi over time, driven by archaea, and not on the reconstruction of the entire microbial community and its change over time. Please replace “microbial” in the title by “archaeal”.

The errors for the δ¹³C_org analyses should be presented (results section and Table 1).

I suggest to include more details on the statistical evaluation (Fig. 5; PCA and correlation matrix) into the methods section.

Why do the authors think the fatty acids <C_16:0 are degraded in the samples? I do not see any indication why this should be the case. The compounds were likely never present or below detection limit.

In section 4.1.1 the authors discuss missing pyrite in some intervals and explain this by too small pyrite aggregates that could not be seen by the naked eye and/or sulfur incorporation into kerogen (l. 406–408). This is pure speculation. The authors could have easily checked the samples for small pyrite aggregates by using thin section microscopy and could have measured the total sulfur content.

The headline of section 4.2 should be changed to something like “The influence of hydrothermal activity on the microbial methane cycle”.

The REE data should be discussed in more detail in section 4.2.

Figures 3 and 4 should be turned 90° and stretched (differences e.g. in interval #1 are barely visible in the current version), with age/depth on the y-axis. It would also be important to include the stratigraphic units and different lithologies.

Please carefully check the color coding of the symbols in figure 6. Shouldn’t the cross at ca. 67% crenarchaeol be green or is the cross incorrect? What about the triangle at ca. 6% GDGT-2 (maybe blue or incorrect symbol)?

Please add some representative GC chromatograms for each interval to the supplement.

Minor comments:
L. 30: Please list some studies that have investigated soda lake sediments/sedimentary rocks over geologic time scales here (some are already mentioned in the manuscript, incl. those from Lake Magadi).
L. 30/31: Delete space before full stop.
L. 87: Delete bracket in front of [2].
L. 92: Replace “microbial” by “archaeal” (please also do so in other relevant areas of the manuscript not mentioned here).
L. 95: The “n” of n-alkanes should be written in italics.
L. 117: Insert space in front of “Although”; delete comma behind “it”.
L. 188–190: Please check for correct phrasing (verb missing?).
L. 282: Please also calculate a mean value without the three outliers.
L. 324–326: Please check for correct phrasing (verb missing?).
L. 336: Replace “microbial” by “archaeal”.
L. 349: Change “biomarkers” to “a potential biomarker”.
L. 350: Change “(FAMEs) were identified” to “(C_17:0 FAME) was identified”.
L. 456: What do the authors mean by the “green checkered pattern”?
L. 606: Replace “predominantly microbial inputs” by “archaeal communities”.
L. 607: Delete “archaeal”.
Figure caption of figure 6: High MI is shown in green, not yellow.
Table 1: It would be great, if the color for “MI on” periods in the table would match the color used in the figures (green).
Citation: https://doi.org/10.5194/egusphere-2024-3006-RC2
- AC2: 'Reply on RC2', Evan Collins, 27 Jan 2025
  
  Hello, please see the attached PDF file for Referee #2.
  
  Citation: https://doi.org/10.5194/egusphere-2024-3006-AC2

Interactive discussion

Status: closed

RC1:
'Comment on egusphere-2024-3006', Anonymous Referee #1, 23 Oct 2024

Please see the attached document.

Citation: https://doi.org/10.5194/egusphere-2024-3006-RC1
- AC1: 'Reply on RC1', Evan Collins, 27 Jan 2025
  
  Hello, please see the attached PDF file for Referee #1.
  
  Citation: https://doi.org/10.5194/egusphere-2024-3006-AC1
RC2:
'Review egusphere-2024-3006', Anonymous Referee #2, 05 Nov 2024
The authors investigated sections of a drill core from Lake Magadi (Hominin Sites and Paleolakes Drilling Project, HSPDP), a soda lake in Kenya, to reconstruct the microbial methane cycle of the lake system over the last 456 ka. The study is focused on molecular biomarker analysis, especially isoGDGTs, representing archaeal core lipids. Together with accompanying (organic-) geochemical data and published information, the authors interpret periodical shifts in microbial methane cycling (and consequently the archaeal community) to be associated with changes in the hydrothermal input at Lake Magadi. It is indicated that phases of low hydrothermal activity show increased microbial methane cycling as compared to phases of high hydrothermal activity.
Soda lakes are important habitats for life. Their investigation, including the microbial methane cycle over time, provides valuable information on these extreme environments and potential early Earth habitats. A detailed reconstruction of the microbial methane cycle of Lake Magadi over time does not exist so far. The findings of the study by Collins et al. are new, complement existing data, and improve our understanding of the Magadi system. The used core samples from the HSPDP are unique, and represent excellent material to study archaeal communities/the microbial methane cycle of Lake Magadi over time. However, the manuscript needs to be substantially improved in some areas before publication:
(i) The sampling strategy is not optimal (cf., l. 129–133). The authors focused on samples that were expected to have high total organic carbon contents (data not presented in the manuscript), which was only assessed by visual inspection (dark brown to black silty clay). The authors argue that those samples would yield the best results. This may have created a biased data set (also samples with low organic carbon contents may show a great molecular diversity). Additionally, the sampling scheme is not consistent. Between the defined intervals #1–6, several meters of core are not covered (3–15 m between single intervals), while within an interval the sampling steps are in parts as close as a few centimeters. It would be interesting to see, if microbial methane cycling was also active during the deposition of sediments with low organic carbon content.
(ii) The study lacks bulk geochemical data of the samples, which would be important to contextualize the presented biomarker and isotope data (e.g., total organic and inorganic carbon carbon contents, total sulfur content, bulk ¹³C_carb). Especially stable carbon isotope data of the carbonate phase (δ¹³C_carb) would improve the discussion of shifts in methane cycling (it seems that at least some samples contain carbonate, as the samples were acid-leached before ¹³C_org analysis; l. 174–175).
(iii) The presented bulk δ¹³C_org data lack context. In lake systems primary production and/or terrestrial input usually govern the carbon cycle. The presented data do not allow the assessment of the role of microbial methane cycling in the lake’s carbon cycle over time. It would help to present total abundances of compounds in relation to the total organic carbon content (amount per g TOC). In addition, the ¹³C_org data should be discussed together with the leaf wax data to evaluate the influence of terrestrial input on the ¹³C_org values. In the presented data set, only three values in interval #2 indicate methanotrophy (−48.1‰, −64.2‰, −89.4‰; Table 1), the rest of the ¹³C_org values could also be explained by variations in primary production and/or terrestrial input.
(iv) The discussion of microbial sulfate reduction in the system (e.g., l. 366–379) is not based on a solid data set. In the current version, only C_17:0 FAME and the appearance of pyrite are used to track microbial sulfate reduction. The C_17:0 FAME, however, is not only produced by sulfate reducers and represents a weak biomarker. Furthermore, it seems that only few samples contain C_17:0 FAME, and it does not necessarily co-occur with pyrite (cf., Table 1). The authors also speculate on the sulfate availability without presenting any robust indication on sulfate levels. Without further data (e.g., sulfur content, stable sulfur isotope composition of the pyrites) this part of the discussion needs to be significantly reduced.
(v) The interpretation of increased microbial methane cycling at times of low hydrothermal input (and vice versa) is mainly based on the correlation of MI with REE data and Ca/Na-ratio. These data sets, however, do not always match (cf., figure 4). The authors should discuss the discrepancies in more detail, and present some explanations for the major discrepancies (e.g., low Ca/Na at the end of interval #2, high Ca/Na together with low REE abundance in interval #5, high REE abundance together with low Ca/Na at the end of interval #6). The MI data set seems to be much more consistent.

More specific comments:
The title is misleading, as the manuscript is focusing on the reconstruction of the microbial methane cycle in Lake Magadi over time, driven by archaea, and not on the reconstruction of the entire microbial community and its change over time. Please replace “microbial” in the title by “archaeal”.

The errors for the δ¹³C_org analyses should be presented (results section and Table 1).

I suggest to include more details on the statistical evaluation (Fig. 5; PCA and correlation matrix) into the methods section.

Why do the authors think the fatty acids <C_16:0 are degraded in the samples? I do not see any indication why this should be the case. The compounds were likely never present or below detection limit.

In section 4.1.1 the authors discuss missing pyrite in some intervals and explain this by too small pyrite aggregates that could not be seen by the naked eye and/or sulfur incorporation into kerogen (l. 406–408). This is pure speculation. The authors could have easily checked the samples for small pyrite aggregates by using thin section microscopy and could have measured the total sulfur content.

The headline of section 4.2 should be changed to something like “The influence of hydrothermal activity on the microbial methane cycle”.

The REE data should be discussed in more detail in section 4.2.

Figures 3 and 4 should be turned 90° and stretched (differences e.g. in interval #1 are barely visible in the current version), with age/depth on the y-axis. It would also be important to include the stratigraphic units and different lithologies.

Please carefully check the color coding of the symbols in figure 6. Shouldn’t the cross at ca. 67% crenarchaeol be green or is the cross incorrect? What about the triangle at ca. 6% GDGT-2 (maybe blue or incorrect symbol)?

Please add some representative GC chromatograms for each interval to the supplement.

Minor comments:
L. 30: Please list some studies that have investigated soda lake sediments/sedimentary rocks over geologic time scales here (some are already mentioned in the manuscript, incl. those from Lake Magadi).
L. 30/31: Delete space before full stop.
L. 87: Delete bracket in front of [2].
L. 92: Replace “microbial” by “archaeal” (please also do so in other relevant areas of the manuscript not mentioned here).
L. 95: The “n” of n-alkanes should be written in italics.
L. 117: Insert space in front of “Although”; delete comma behind “it”.
L. 188–190: Please check for correct phrasing (verb missing?).
L. 282: Please also calculate a mean value without the three outliers.
L. 324–326: Please check for correct phrasing (verb missing?).
L. 336: Replace “microbial” by “archaeal”.
L. 349: Change “biomarkers” to “a potential biomarker”.
L. 350: Change “(FAMEs) were identified” to “(C_17:0 FAME) was identified”.
L. 456: What do the authors mean by the “green checkered pattern”?
L. 606: Replace “predominantly microbial inputs” by “archaeal communities”.
L. 607: Delete “archaeal”.
Figure caption of figure 6: High MI is shown in green, not yellow.
Table 1: It would be great, if the color for “MI on” periods in the table would match the color used in the figures (green).
Citation: https://doi.org/10.5194/egusphere-2024-3006-RC2
- AC2: 'Reply on RC2', Evan Collins, 27 Jan 2025
  
  Hello, please see the attached PDF file for Referee #2.
  
  Citation: https://doi.org/10.5194/egusphere-2024-3006-AC2

Peer review completion

AR: Author's response | RR: Referee report | ED: Editor decision | EF: Editorial file upload

ED: Reconsider after major revisions (11 Feb 2025) by Sebastian Naeher

Dear Dr Collins et al.,

Thanks for the submission of this interesting manuscript to Biogeosciences and for your responses to the feedback that we received from two reviewers. I agree with the reviewers in tending to recommend more major revision is required. I think the reviewers raise several good questions and provide helpful comments. I get quite a good idea of how you plan to revise your manuscript accordingly and invite you to submit your revised manuscript that incorporates these improvements.

I generally agree with the reviewer feedback and your responses, and many of my own questions are already covered, so I will not repeat them here. A few additional comments though:

I understand why you intend to remove the FA and alkane data and am okay with your decision, though admittedly not with a strong preference either way. I guess it would be good to keep these data included in the manuscript if you had additional compound-specific d13C data (also from compounds such as archaeol, hydroxyarchaeol, crocetane, PMIs, unsaturated C16 and C18 FAs, iso and anteiso FAs, etc, if present), because then you could make a more thorough assessment of relative abundances of authochthonous and allochthonous sources, which would further illustrate that there are only low contributions of terrestrial OM.

You could also use brGDGTs to get an idea of terrestrial/soil OM inputs and summarise this briefly in the manuscript as alternative to other biomarker data? The BIT index is unlikely to be useful, but the ratio of iso/br or other proxies reported in the literature may help with this?

Furthermore, you could get a better understanding of changing communities and better distinguish methanogenic from methanotrophic bacteria, SRB and methanotrophic bacteria that live in the sediments and/or water column using CSIA data of above mentioned compounds. This would be helpful to better understand the processes of "switch on/off" of methane production and consumption in the lake and in strong contrast to the hydrothermal periods. This is probably out of scope for the current manuscript, but could be considered for future work.

Thank you and I look forward to your revised manuscript.

Kind regards,
Dr Sebastian Naeher
Associate Editor, Biogeosciences.

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AR by Evan Collins on behalf of the Authors (14 Mar 2025) Author's response

EF by Katja Gänger (20 Mar 2025) Supplement

EF by Katja Gänger (20 Mar 2025) Manuscript

EF by Katja Gänger (20 Mar 2025) Author's tracked changes

ED: Referee Nomination & Report Request started (24 Mar 2025) by Sebastian Naeher

RR by Anonymous Referee #2 (03 Apr 2025)

RR by Anonymous Referee #1 (03 Apr 2025)

ED: Publish subject to minor revisions (review by editor) (07 Apr 2025) by Sebastian Naeher

AR by Evan Collins on behalf of the Authors (22 Apr 2025) Author's response Author's tracked changes Manuscript

ED: Publish subject to technical corrections (22 Apr 2025) by Sebastian Naeher

AR by Evan Collins on behalf of the Authors (05 May 2025) Author's response Manuscript

Journal article(s) based on this preprint

14 Aug 2025

Hot-spring inputs and climate drive dynamic shifts in archaeal communities in Lake Magadi, Kenya Rift Valley

Evan R. Collins, Troy M. Ferland, Isla S. Castañeda, R. Bernhart Owen, Tim K. Lowenstein, Andrew S. Cohen, Robin W. Renaut, Molly D. O'Beirne, and Josef P. Werne

Biogeosciences, 22, 3931–3948, https://doi.org/10.5194/bg-22-3931-2025,https://doi.org/10.5194/bg-22-3931-2025, 2025

Short summary

Evan R. Collins, Troy M. Ferland, Isla S. Castañeda, R. Bernhart Owen, Tim K. Lowenstein, Andrew S. Cohen, Robin W. Renaut, Molly D. O'Beirne, and Josef P. Werne

Supplement

https://doi.org/10.5194/egusphere-2024-3006-supplement

Evan R. Collins, Troy M. Ferland, Isla S. Castañeda, R. Bernhart Owen, Tim K. Lowenstein, Andrew S. Cohen, Robin W. Renaut, Molly D. O'Beirne, and Josef P. Werne

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Short summary

Archaeal molecular fossils (tetraethers) have been used around the globe to track changes in climate. Little is known about archaeal response to environmental change in soda lakes, especially lakes influenced by hydrothermal inputs. For the first time in Lake Magadi, we show tetraethers tracking abrupt changes in methane and non-methane producers due to hydrothermal inputs to the lake. This study provides insight into the role of hydrothermal water sources and methane production in soda lakes.

Hydrothermal inputs drive dynamic shifts in microbial communities in Lake Magadi, Kenya Rift Valley

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