the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
| 14 Mar 2025
A niche for diverse cable bacteria in continental margin sediments overlain by oxygen-deficient waters
Abstract. Since the discovery of cable bacteria more than a decade ago, these multi-cellular, filamentous sulfur-oxidizing bacteria have been found in a range of sedimentary environments. However, their abundance, diversity and activity in continental margin sediments overlain by oxygen-deficient waters at water depths >100 m remain poorly known. Here we address this by studying five basins along the coasts of California and Mexico. All sediments are organic carbon rich (2.5 – 7.5 wt%) and characterized by active iron and sulfur cycling. Nitrate is present in the bottom water at all sites. Results of fluorescence in-situ hybridization (FISH) indicate a low areal abundance of cable bacteria (0.2 to 19 m cm-2) in sediments of the hypoxic San Clemente, Catalina and San Pedro basins and anoxic San Blas basin. In the anoxic Soledad basin, in contrast, we found abundant cable bacteria near the sediment surface (129 m cm-2). DNA amplicon sequencing detected cable bacteria reads in sediments of the hypoxic San Pedro, and anoxic Soledad and San Blas basins. Phylogenetic analysis indicated that the diversity of the amplicon sequence variants (ASVs) was spread across the Candidatus Electrothrix lineage, including multiple ASVs closely related to Electrothrix gigas, a recently discovered species of giant cable bacteria. Additionally, multiple sequences retrieved from the Soledad and San Blas basins revealed affiliation with a clade sister to Electrothrix, hypothesized as a novel genus, suggesting possible relic or novel adaptations of cable bacteria to these anoxic and nitrogenous environments. The areal abundance of cable bacteria was negatively related to sediment Fe/S ratios suggesting a control by sulfide availability. Free sulfide in the porewater was only detected at the anoxic Soledad site, however. Micro-profiling of pH and electric potential point towards a lack of cable bacteria activity at the time of sampling, possibly due to a limitation by a suitable electron donor and/or acceptor. Periodically enhanced organic matter input and associated sulfate reduction and/or inflows of oxic water could alleviate the deficiency, creating the observed niche for diverse cable bacteria.
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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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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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- Final revised paper
Journal article(s) based on this preprint
Interactive discussion
Status: closed
-
RC1: 'Comment on egusphere-2025-817', Maxime Daviray, 15 Apr 2025
- AC1: 'Reply on RC1', Caroline P. Slomp, 14 May 2025
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RC2: 'Comment on egusphere-2025-817', Anonymous Referee #2, 18 Apr 2025
Review of Slomp et al. A niche for diverse cable bacteria in continental margin sediments overlain by oxygen-deficient waters.
The manuscript of Slomp et al. describes a study where activity and abundance of Cabel bacteria were addressed in sediments from 5 hypoxic basins along the coast of Mexico and California, together with a multitude of geochemical features (O2, pH, Fe, Mn, Nox, Al ) and microbial populations. In general cable bacteria abundance were low and activity were below detection limit. Phylogenetic analysis revealed that the Cable bacteria belonged to the Candidatus Electrotrix lineage and included specimens affiliated with Electrotrix gigas. In addition several sequences were affiliated with a sister clade to Electrotrix and it is suggested that these represent a novel genius.
In general, the manuscript adds novel information about the biogeography and diversity of cable bacteria in marine environments and has therefore merits justifying publication. I recommend however that the authors put somewhat more effort in discussing the vast amount of geochemical data and provide the motivation behind the analysis these features. There are severall fractions of solidphase and dissolved compounds that is not (to my knowledge )really linked to cable bacteria (e.g. Al, Mn, NH4 ): Why is this relevant in the given context?; What was the hypothesis? In addition the motivation behind the analysis of the general microbial community should be stated more clear. What is the relevance of this analysis for the target features: cable bacteria?
In my view these data should be more integrated in the overall framework of the study:
Would it e.g. be possible to apply e.g. network analysis to identify specific cablebacteria – microbe associations?
Minor:
L 32: remove the Nielsen et al . 2010 reference. This paper says nothing about cable bacteria. The authors suggest nanowires or conductive minerals as mediators of the electric currents that runs through the sediment (exactly like in the Revil et al. (2010) paper!) The discovery of cable bacteria was published in 2012. i.e. two years after the Nielsen et al. paper.
L 34: Remove the reference Nielsen and Risgaard-Petersen 2015 paper: This is a review paper that amongst other review the Risgaard-Petersen et al. 2012 paper on how cable bacteria influence the biogeochemistry.
L 49. The Damgaard et al 2014 paper describes the construction and application of the silver silver chloride electrode used for electric potential measurements. The focus in this paper is not relationships between cable bacteria activity and the electric potential. Such is more thoroughly described in Risgaard-Petersen et al. (2012) and in Risgaard-Petersen et al. (2014). Since both papers precedes the Damgaard et al. paper I suggest that that the authors include those here instead of the Damgaard et al. paper.
L 133. Please spell out “EP”: Electric potential.
L150: What sediment volume was collected for FISH: 0.5 ml?? Please specify.
L 195. The method description for quantitative FISH analysis is a bit odd. What is the rational for not using direct methods like those described in e.g. Schauer et al. (2014)?. Why use Nycodens extractions? There is to my experience a great risk of loosing cells with this method. Do the authors have any data on the cell recovery efficacy ?
It apereas that Sybr Green I staining were used for Cable bacteria quantification : Why this step when you have FISH stained filaments already?
References
Revil, A., Mendonca, C.A., Atekwana, E.A., Kulessa, B., Hubbard, S.S., Bohlen, K.J., 2010. Understanding biogeobatteries: Where geophysics meets microbiology. J. Geophys. Res. (Biogeosci.) 115, G00G02.
Risgaard-Petersen, N., Damgaard, L.R., Revil, A., Nielsen, L.P., 2014. Mapping electron sources and sinks in a marine biogeobattery. J. Geophys. Res. (Biogeosci.) 119 1475–1486.
Risgaard-Petersen , N., Revil, A., Meister, P., Nielsen, L.P., 2012. Sulfur, iron-, and calcium cycling associated with natural electric currents running through marine sediment. Geochimica Et Cosmochimica Acta 92, 1-13.
Schauer, R., Risgaard-Petersen, N., Kjeldsen, K.U., Bjerg, J.J.T., Jørgensen, B.B., Schramm, A., Nielsen, L.P., 2014. Succession of cable bacteria and electric currents in marine sediment. Isme Journal 8, 1314-1322.
Citation: https://doi.org/10.5194/egusphere-2025-817-RC2 - AC2: 'Reply on RC2', Caroline P. Slomp, 14 May 2025
Interactive discussion
Status: closed
-
RC1: 'Comment on egusphere-2025-817', Maxime Daviray, 15 Apr 2025
General comments:
In this manuscript, Slomp et al. initially described the continental margin sediments (>100 m deep) of hypo- to anoxic nitrogenous basins as a niche for the development of cable bacteria (CB). Then, they estimated the abundance and diversity within the Cadidatus Electrothrix lineage to provide an overview of the recently described diversity of this group, and to suggest a new genus adapted to these environmental conditions. The manuscript is fairly well structured, and its objectives are clear. The methodological approaches are comprehensive and aim to characterise the geochemical conditions of the bottom waters, the sedimentary compartment (pore-water and solid phases) and the microbial community concerned. The data sets are freely accessible on Zenodo. Despite the wide range and quality of the data, it is a snapshot in time, which limits the scope of the discussion on the factors controlling the CB dynamics in this potential niche. Overall, I think this is a robust and very interesting research paper which corresponds to the scope of Biogeosciences.
Specific comments:
Line 104: you present bibliographical data on Thioploca in the Soledad basin, but nothing on the other groups presented in the introduction (Beggiatoaceae and Thiomargarita). Is there any information available on this subject in these basins? Similarly, in line 108, you present (admittedly old) data on the meiofauna and macrofauna of this same basin, but you say nothing about the other basins? Have no data been published?
Lines 133-135: only one O2 profile was done in San Clemente? How were the pH and H2S measurements set up to achieve complete microprofiling to a depth of over 3 cm in less than 15 minutes? I assume that the waiting and measurement times are particularly short. Is this relevant for this type of measurement?
Line 160: one point I don't understand about the analysis of dissolved metals: why didn't you use the pore water Mn data from Bruggmann et al. (2023), as you did for Fe, in order to have the same vertical resolution for both? The vertical resolution in Bruggmann et al. (2023) is low and I find it relevant that you have carried out higher resolution analyses for Mn. But in that case, why didn't you do the same for Fe to get geochemistry within the same core?
Section 4.1: the densities observed in these hypo-anoxic basins are like those observed in situ on estuarine intertidal mudflats (oxygenated environment + sulphides) where CB could be particularly active (Daviray et al., 2024), or in the rhizosphere of aquatic plants (Scholz et al., 2019, 2021).
The presence of CB (DNA data) but the absence of activity also raises a hypothesis that is not discussed here: could it be the result of CB-enriched sediment transport into the basins? Do you have any information on the marine currents affecting these locations? In this case, it could be better to talk about a ‘potential’ niche.
Section 4.2: The discussion of the sources of H2S and its temporal dynamics is stimulating. However, it remains hypothetical and suffers from a lack of (temporal) data, in my opinion. Have you tested correlations between the various parameters (i.e., Corg, total S, Fe sulphides, etc.) to perhaps highlight this dynamic and support a periodic (seasonal?) increase in sulphate reduction?
Lines 434-447: in my opinion, this paragraph lacks any link with the biogeochemical data to explain the diversity observed.
Line 441: what electron acceptor do the Bacteroidota use?
Line 453: it's a shame that we don't have this data, as it would have helped to underpin the discussion on interspecific competition.
Line 461: any suggestions on these factors (bioturbation or others generating sediment heterogeneity, Fe curtain, etc.)?
Lines 475-476: out of curiosity, do you have any idea what these benefits might be? The same for the selective pressures mentioned line 489. The section 4.4 is very interesting and frustrating: we want to know more!
Section 4.5: this section could perhaps be further summarised and incorporated into the second paragraph of the conclusion.
Figures:
Figure 1: the blue colour contrast is poor. Would it be possible to improve it like in Bruggmann et al., 2023?
Figure 2: you write that triplicates were achieved for pH and H2S µprofiles. Is the absence of standard deviation on these profiles justified by their high reproducibility? I suppose so for H2S (because there isn't any), but what about pH?
Figures 2, 3 and 4: please, put the unit of the vertical axis in cm.
Citation: https://doi.org/10.5194/egusphere-2025-817-RC1 - AC1: 'Reply on RC1', Caroline P. Slomp, 14 May 2025
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RC2: 'Comment on egusphere-2025-817', Anonymous Referee #2, 18 Apr 2025
Review of Slomp et al. A niche for diverse cable bacteria in continental margin sediments overlain by oxygen-deficient waters.
The manuscript of Slomp et al. describes a study where activity and abundance of Cabel bacteria were addressed in sediments from 5 hypoxic basins along the coast of Mexico and California, together with a multitude of geochemical features (O2, pH, Fe, Mn, Nox, Al ) and microbial populations. In general cable bacteria abundance were low and activity were below detection limit. Phylogenetic analysis revealed that the Cable bacteria belonged to the Candidatus Electrotrix lineage and included specimens affiliated with Electrotrix gigas. In addition several sequences were affiliated with a sister clade to Electrotrix and it is suggested that these represent a novel genius.
In general, the manuscript adds novel information about the biogeography and diversity of cable bacteria in marine environments and has therefore merits justifying publication. I recommend however that the authors put somewhat more effort in discussing the vast amount of geochemical data and provide the motivation behind the analysis these features. There are severall fractions of solidphase and dissolved compounds that is not (to my knowledge )really linked to cable bacteria (e.g. Al, Mn, NH4 ): Why is this relevant in the given context?; What was the hypothesis? In addition the motivation behind the analysis of the general microbial community should be stated more clear. What is the relevance of this analysis for the target features: cable bacteria?
In my view these data should be more integrated in the overall framework of the study:
Would it e.g. be possible to apply e.g. network analysis to identify specific cablebacteria – microbe associations?
Minor:
L 32: remove the Nielsen et al . 2010 reference. This paper says nothing about cable bacteria. The authors suggest nanowires or conductive minerals as mediators of the electric currents that runs through the sediment (exactly like in the Revil et al. (2010) paper!) The discovery of cable bacteria was published in 2012. i.e. two years after the Nielsen et al. paper.
L 34: Remove the reference Nielsen and Risgaard-Petersen 2015 paper: This is a review paper that amongst other review the Risgaard-Petersen et al. 2012 paper on how cable bacteria influence the biogeochemistry.
L 49. The Damgaard et al 2014 paper describes the construction and application of the silver silver chloride electrode used for electric potential measurements. The focus in this paper is not relationships between cable bacteria activity and the electric potential. Such is more thoroughly described in Risgaard-Petersen et al. (2012) and in Risgaard-Petersen et al. (2014). Since both papers precedes the Damgaard et al. paper I suggest that that the authors include those here instead of the Damgaard et al. paper.
L 133. Please spell out “EP”: Electric potential.
L150: What sediment volume was collected for FISH: 0.5 ml?? Please specify.
L 195. The method description for quantitative FISH analysis is a bit odd. What is the rational for not using direct methods like those described in e.g. Schauer et al. (2014)?. Why use Nycodens extractions? There is to my experience a great risk of loosing cells with this method. Do the authors have any data on the cell recovery efficacy ?
It apereas that Sybr Green I staining were used for Cable bacteria quantification : Why this step when you have FISH stained filaments already?
References
Revil, A., Mendonca, C.A., Atekwana, E.A., Kulessa, B., Hubbard, S.S., Bohlen, K.J., 2010. Understanding biogeobatteries: Where geophysics meets microbiology. J. Geophys. Res. (Biogeosci.) 115, G00G02.
Risgaard-Petersen, N., Damgaard, L.R., Revil, A., Nielsen, L.P., 2014. Mapping electron sources and sinks in a marine biogeobattery. J. Geophys. Res. (Biogeosci.) 119 1475–1486.
Risgaard-Petersen , N., Revil, A., Meister, P., Nielsen, L.P., 2012. Sulfur, iron-, and calcium cycling associated with natural electric currents running through marine sediment. Geochimica Et Cosmochimica Acta 92, 1-13.
Schauer, R., Risgaard-Petersen, N., Kjeldsen, K.U., Bjerg, J.J.T., Jørgensen, B.B., Schramm, A., Nielsen, L.P., 2014. Succession of cable bacteria and electric currents in marine sediment. Isme Journal 8, 1314-1322.
Citation: https://doi.org/10.5194/egusphere-2025-817-RC2 - AC2: 'Reply on RC2', Caroline P. Slomp, 14 May 2025
Peer review completion
Journal article(s) based on this preprint
Data sets
Datafile_Cable bacteria manuscript_Slomp et al.xlsx C. P. Slomp et al. https://doi.org/10.5281/zenodo.14896362
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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
(2012 KB) - Metadata XML
-
Supplement
(2000 KB) - BibTeX
- EndNote
- Final revised paper
General comments:
In this manuscript, Slomp et al. initially described the continental margin sediments (>100 m deep) of hypo- to anoxic nitrogenous basins as a niche for the development of cable bacteria (CB). Then, they estimated the abundance and diversity within the Cadidatus Electrothrix lineage to provide an overview of the recently described diversity of this group, and to suggest a new genus adapted to these environmental conditions. The manuscript is fairly well structured, and its objectives are clear. The methodological approaches are comprehensive and aim to characterise the geochemical conditions of the bottom waters, the sedimentary compartment (pore-water and solid phases) and the microbial community concerned. The data sets are freely accessible on Zenodo. Despite the wide range and quality of the data, it is a snapshot in time, which limits the scope of the discussion on the factors controlling the CB dynamics in this potential niche. Overall, I think this is a robust and very interesting research paper which corresponds to the scope of Biogeosciences.
Specific comments:
Line 104: you present bibliographical data on Thioploca in the Soledad basin, but nothing on the other groups presented in the introduction (Beggiatoaceae and Thiomargarita). Is there any information available on this subject in these basins? Similarly, in line 108, you present (admittedly old) data on the meiofauna and macrofauna of this same basin, but you say nothing about the other basins? Have no data been published?
Lines 133-135: only one O2 profile was done in San Clemente? How were the pH and H2S measurements set up to achieve complete microprofiling to a depth of over 3 cm in less than 15 minutes? I assume that the waiting and measurement times are particularly short. Is this relevant for this type of measurement?
Line 160: one point I don't understand about the analysis of dissolved metals: why didn't you use the pore water Mn data from Bruggmann et al. (2023), as you did for Fe, in order to have the same vertical resolution for both? The vertical resolution in Bruggmann et al. (2023) is low and I find it relevant that you have carried out higher resolution analyses for Mn. But in that case, why didn't you do the same for Fe to get geochemistry within the same core?
Section 4.1: the densities observed in these hypo-anoxic basins are like those observed in situ on estuarine intertidal mudflats (oxygenated environment + sulphides) where CB could be particularly active (Daviray et al., 2024), or in the rhizosphere of aquatic plants (Scholz et al., 2019, 2021).
The presence of CB (DNA data) but the absence of activity also raises a hypothesis that is not discussed here: could it be the result of CB-enriched sediment transport into the basins? Do you have any information on the marine currents affecting these locations? In this case, it could be better to talk about a ‘potential’ niche.
Section 4.2: The discussion of the sources of H2S and its temporal dynamics is stimulating. However, it remains hypothetical and suffers from a lack of (temporal) data, in my opinion. Have you tested correlations between the various parameters (i.e., Corg, total S, Fe sulphides, etc.) to perhaps highlight this dynamic and support a periodic (seasonal?) increase in sulphate reduction?
Lines 434-447: in my opinion, this paragraph lacks any link with the biogeochemical data to explain the diversity observed.
Line 441: what electron acceptor do the Bacteroidota use?
Line 453: it's a shame that we don't have this data, as it would have helped to underpin the discussion on interspecific competition.
Line 461: any suggestions on these factors (bioturbation or others generating sediment heterogeneity, Fe curtain, etc.)?
Lines 475-476: out of curiosity, do you have any idea what these benefits might be? The same for the selective pressures mentioned line 489. The section 4.4 is very interesting and frustrating: we want to know more!
Section 4.5: this section could perhaps be further summarised and incorporated into the second paragraph of the conclusion.
Figures:
Figure 1: the blue colour contrast is poor. Would it be possible to improve it like in Bruggmann et al., 2023?
Figure 2: you write that triplicates were achieved for pH and H2S µprofiles. Is the absence of standard deviation on these profiles justified by their high reproducibility? I suppose so for H2S (because there isn't any), but what about pH?
Figures 2, 3 and 4: please, put the unit of the vertical axis in cm.