the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
| 27 Feb 2023
What is eating my rocks? A possible novel biological niche in limestone
Abstract. Metamorphic limestones in Namibia and Oman were found to be consumed inside the rock mass by microbiological activity of a thus far unknown nature that created bands of parallel tubules. Tubule of up to 0.5 mm wide and 30 mm long collectively form bands of tens of meters long. These bands formed along fractures in the rock and only surfaced after erosion. In fresh outcrops the tubules are filled with white calcium carbonate with internal structures. This filling is depleted for several metal elements that can be incorporated into biomatter and was deposited by the microorganisms as they grew inside the rock. The rim of the tubules contain1 µm wide growth rings enriched for P and S. Fluorescence microscopy confirmed presence of biological material. The rocks are too old to conserve DNA or protein. We consider this a new niche for life that has so far not been described.
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RC1: 'Comment on bg-2023-32', Anonymous Referee #1, 29 Mar 2023
The authors describe a special type of caliche-calcrete crust, which is often found in hot arid, desert-like areas. These crusts are partially laminated (partly "endostromatolites" whatever this means) with tubular hollow structures up to several centimeters long found on bedrock carbonate surfaces. These structures are probably solution structures caused by organisms that have massively dissolved underlying bedrock carbonate layers. Some of the tube-cavities have been already backfilled or cemented. The cement crusts are enriched in certain elements that were originally enriched in the bedrock carbonate layers. The authors observed enrichments of P and S in some areas and interpret these element enrichments as a biosignature. They also observed autofluorescence in some the special caliche cement crusts, which they attribute to organic material incorporated in the carbonates. The age of the caliche is not known, but could be carried out using 14C and/or other methods. Presumably they are Quaternary formations especially formed during humid climatic phases.
The concept of a “new” biological niche without providing any evidence of life is very optimistic and in this form not acceptable. The manuscript has considerable methodological deficiencies. If it is claimed that microorganisms that have produced these caliche tube structure-microbialites, it is imperative that the possibilities of modern bio-geochemical analyses be applied to test this assumption. Following analytical procedures should be used and tested:
1: Raman spectroscopy to test mineral inventory and organic carbon content in the carbonate minerals in caliche and bedrock
2: Application of geo-histological techniques (histochemical staining procedures for organic residues).
3: Stable C-O-S isotope analyses of caliche carbonates und bedrock carbonates to detect possible metabolic fractionation in caliche and bedrock.
4: Lipid biomarker analyses of caliche rocks looking for prokaryote (bacteria + archaea) and eukaryote (e.g. fungi!-lichens) organism traces.
Autofluorescence effects can also be produced by certain minerals and not necessarily by organic molecules only. Authors must check the literature
The manuscript is not publishable in its present form. The authors have to prove which organism groups were likely involved in the formation of these structures. Probably lichen communities may have played a significant role. The analytical possibilities mentioned above open up possibilities of a comprehensible interpretation.
Citation: https://doi.org/10.5194/bg-2023-32-RC1 -
AC1: 'Reply on RC1', Cees Passchier, 15 May 2023
We thank the reviewers for their comments. We appreciate their concerns, but we feel that the most important message of our manuscript has somehow not reached them, namely that no known geological process can explain the observations we describe in our manuscript.
Two of the authors are highly experienced geologists with many years of field experience, and are specialists in metamorphic rocks (JU and CWP). Of course, the authors are aware that fluorescence can be caused by crystalline material (a speciality of author AJ), and that trace elements of S or P can be present in carbonates (something NG and RM-K are also highly familiar with). But what is crucial here is that pores or tubules that form inside a carbonate rock similar to what we described have apparently never before been described. We cannot think of any geological process that can describe the formation of the presented tubules, hence we proposed a biological origin. The structures are apparently fossils, which may or may not still contain recognisable organic material.
The reviewers are correct that the evidence is not conclusive. But we consider this descriptive manuscript as a start, to clearly describe and present the observations. In addition, these must then be interpreted, which is what we did here. Only then can funding be applied for, after which more elaborate and expensive methodology can be used to elucidate the proposed biological origin. We consider this an opportunity that might open a completely novel research subject, and we wish to share our observations with the scientific community. It is a bit of a disappointment that the two reviewers would not allow such an opportunity. One can only imagine what the outcome of a grant review process would be, if we were to apply for money to further investigate this, without any evidence that the observations have been shared with the scientific community. As such, we think it important that our basic geometric observations are published, in order to give other scientists a chance to react and open a discussion what these structures could be.
Below, we address the points raised in more detail.
Reviewer 1:
The authors describe a special type of caliche-calcrete crust, which is often found in hot arid, desert-like areas. These crusts are partially laminated (partly "endostromatolites" whatever this means) with tubular hollow structures up to several centimeters long found on bedrock carbonate surfaces. These structures are probably solution structures caused by organisms that have massively dissolved underlying bedrock carbonate layers. Some of the tube-cavities have been already backfilled or cemented. The cement crusts are enriched in certain elements that were originally enriched in the bedrock carbonate layers. The authors observed enrichments of P and S in some areas and interpret these element enrichments as a biosignature. They also observed autofluorescence in some the special caliche cement crusts, which they attribute to organic material incorporated in the carbonates. The age of the caliche is not known, but could be carried out using 14C and/or other methods. Presumably they are Quaternary formations especially formed during humid climatic phases.
AU response: endostromatolites are mentioned in the reference list. In view of the age of the investigated rocks, 14C dating is difficult because of the large amount of "dead carbon" present in the marble, which would swamp any attempt at dating; we do not see a way to separate the marble from any organic carbon that may be present. In any case, any biological material is most likely fossilized and present in minute amounts, for which the aging methods are not sensitive enough. Also, dating will not solve the riddle of how the observed tubules were formed.
The concept of a “new” biological niche without providing any evidence of life is very optimistic and in this form not acceptable.
AU response: we may have been bold in proposing an entirely new lifeform: what we propose is that we see unexplained structures which are probably of biological origin, and for which we give a tentative explanation. As stated above, an explanation must be given how the observed cavities were formed, and a geological, abiotic explanation is not available. That we propose this as a biological niche is simply in lack of a more plausible explanation not involving micro-organisms. We could be less bold in our manuscript and just ask a simple question: does any specialist in calcrete/carbonate studies who works in deserts know these kinds of structures? Have they ever been described before? Are there specialised labs who would like to further investigate them? But a manuscript only presenting questions and not giving a possible explanation, how unlikely (in the eyes of some) it be, is not providing much progress either. Therefore, we decided to include a description of how these pores and tubules might have formed.
The manuscript has considerable methodological deficiencies. If it is claimed that microorganisms that have produced these caliche tube structure-microbialites, it is imperative that the possibilities of modern bio-geochemical analyses be applied to test this assumption. Following analytical procedures should be used and tested:
1: Raman spectroscopy to test mineral inventory and organic carbon content in the carbonate minerals in caliche and bedrock
AU response: we have applied RAMAN, and although the fluorescence is very strong in the samples, hampering the analysis, we see evidence of elemental C being present, which may be interpreted as fossilized organic material. We can incorporate this in a revised manuscript, but we are not sure this would convince the reviewer.
2: Application of geo-histological techniques (histochemical staining procedures for organic residues).
AU response: Histochemical staining is overly optimistic, as the fossilized organic material is most likely completely decomposed.
3: Stable C-O-S isotope analyses of caliche carbonates und bedrock carbonates to detect possible metabolic fractionation in caliche and bedrock.
AU response: One of the authors (CWP) is a specialist on stable C/O isotope analysis in carbonates and from experience can say that far more material is required for any outcome by this kind of analysis than the tubules can produce. The tubules are very small and only affect a small band in the marbles – any material left behind would be of microscopic quantity only.
4: Lipid biomarker analyses of caliche rocks looking for prokaryote (bacteria + archaea) and eukaryote (e.g. fungi!-lichens) organism traces.
AU response: Again, it is highly unlikely to find lipid biomarkers in these ancient, fossilized rocks.
Autofluorescence effects can also be produced by certain minerals and not necessarily by organic molecules only. Authors must check the literature
AU response: The authors are very much aware of autofluorescence and based on many, many years of experience, we can assure the reviewer that this is not behind the observations. Fluorescent minerals never form tubules, and never form the growth-layer structure on a microscopic scale as we have observed and described here.
The manuscript is not publishable in its present form. The authors have to prove which organism groups were likely involved in the formation of these structures. Probably lichen communities may have played a significant role. The analytical possibilities mentioned above open up possibilities of a comprehensible interpretation.
AU response: It is interesting that on the one hand the reviewer is reluctant to accept a biological origin, and on the other hand proposes that ‘lichen communities [probably] may have played a significant role’. The key point here is that we propose a model how microbiological activity (which we don’t want to pin down on fungi, lichen, archaea or bacteria) can form cavities that are visible by naked eye. That we don’t know which life form was responsible for the formation of these cavities doesn’t mean one can’t speculate that a life form was responsible. If we were to only present the observations without any explanation, simply describing a geometry and asking the question - what is this? (biotic or abiotic), a reviewer would most likely demand an explanation.
Reviewer 2.
This manuscript presents an interesting observation of the tubular structures found in metamorphic rocks in Namibia and Oman in similar arid desert areas. The tubular structures are partially laminated, located along rock fractures, and surfaced after erosion. In the fresh outcrops, the tubular structures were filled with calcite and depleted on some metals. The authors applied Laser Ablation-Inductively Coupled Plasma Mass Spectrometry, Electron Microprobe Analysis and fluorescence microscopy as imaging techniques to analyze the structures.
The authors observed enrichment in P and S at the rim of some filling and the depletion of Sr, Mn, Fe and some Rare Earth elements (Nd, Th, Ce, Pr, La) in the white materials.
The authors speculated on the "biological" nature of the observed structures. However, no evidence supports the conceptual model (Figure 10). No one technique has been applied to prove the organic origin of P and S in the tubular structures. P and S can also be part of minerals, and autofluorescence signals can be emitted from minerals.AU response: as stated above, describing the observations without any possible explanation how they arose (as unlikely as the explanation may seem) is not very satisfactory. A conceptual model was proposed to explain how macroscopic structures can be formed by microscopic organisms. The authors are aware that P and S can be ‘part of minerals’ and that minerals can cause autofluorescence. That is not what we see here, a statement that is based on years of experience in carbonate microscopy. No known mineral spontaneously grows in the shapes we have observed and described here.
It is also not feasible that water entering fractures will create equidistant distances between tubular, and it is also speculative that microbial cells growing there remain P and S and leave calcite. The authors also suggested that "In addition to growth in the longitudinal direction, radial growth would widen the tubule (Fig. 10C), and this requires Ca transport towards the centre of the cavity, where over time a column is formed that fills the tubule". It is unclear how and why Ca will transport to the centre of the cavity, and the suggested mechanism cannot explain the rows of tubular of approximately similar diameter.
AU response: The equidistant position of the tubules was not the result of water entering fractures, but may have been caused by nutrient competition of starting communities. That Ca transport is needed towards the centre is a result of how the hypothesized community would grow: it starts at the centre, but grows radially out of this centre. In order to make space, material that can’t be incorporated into biomatter (here, Ca) must be deposited, which can be done at the centre, where growth is no longer possible, as all nutrients have been used. A single layer of microorganisms wouldn’t require much Ca transport, but would not produce pores that are macroscopically visible.
The manuscript contains many speculations, e.g., that the microbes may be a monoculture.AU response: Either microbes are a monoculture or they are a complex community. We tried to start with the simplest possibility, that of a monoculture. Of course, a more complex community is also possible, in which case multiple species would have to reach the niche simultaneously or sequentially.
Since the manuscript has no evidence for the main statement about the biological origin of the tubules in metamorphic limestone in Namibia and Oman, I do not recommend the manuscript for publication.AU response: This boils down to what we state at the beginning of this letter: there is simply no geological explanation for these tubules. This is a completely novel observation, though it is not unique to one rock or one location. Sometimes, a novelty is just that: something not yet described. And what authors are supposed to do in that case is clearly describe what they observe, and interpret their findings as best as they can. We accept that our explanation is speculative, but again, no other explanation can be given (not by us, and apparently also not by the reviewers).
The authors need to bring evidence for their statement. For example, the analysis of biomarkers, Raman mapping and isotopic analysis are required to check the chemical structure of organic matter. I suggest applying some high spatial resolution techniques to support the microbial origin. , e.g., Nano-SIMS.AU response: Once our findings are published, one can start to consider applying for grants to investigate this further, or collaborate with others who have the facilities and interest to do so. Without a publication, there is no chance that we, or others (and we are happy to share our rock samples with other scientists) can raise funding for further analyses, which, as this reviewer is surely aware of, are not cheap, and can be really challenging when dealing with microscopic amounts of material only.
Summarising:
We have the impression that the reviewers were irritated by our interpretation of the tubular structures we found. We propose this interpretation because we thought reviewers would even be more irritated by a mere description of unknown features, without any attempt at interpretation. Our main concern is to bring these unknown features to the attention of the scientific community to hear if, with our combined experience, there are scientists who do know these features, or know in which direction to further research them. More detailed analyses as proposed by the reviewers should be attempted, but we believe the first step is to publish the geometry and overall properties of this unknown and novel phenomenon.
Since the manuscript has no evidence for the main statement about the biological origin of the tubules in metamorphic limestone in Namibia and Oman, I do not recommend the manuscript for publication.AU response: This boils down to what we state at the beginning of this letter: there is simply no geological explanation for these tubules. This is a completely novel observation, though it is not unique to one rock or one location. Sometimes, a novelty is just that: something not yet described. And what authors are supposed to do in that case is clearly describe what they observe, and interpret their findings as best as they can. We accept that our explanation is speculative, but again, no other explanation can be given (not by us, and apparently also not by the reviewers).
The authors need to bring evidence for their statement. For example, the analysis of biomarkers, Raman mapping and isotopic analysis are required to check the chemical structure of organic matter. I suggest applying some high spatial resolution techniques to support the microbial origin. , e.g., Nano-SIMS.AU response: Once our findings are published, one can start to consider applying for grants to investigate this further, or collaborate with others who have the facilities and interest to do so. Without a publication, there is no chance that we, or others (and we are happy to share our rock samples with other scientists) can raise funding for further analyses, which, as this reviewer is surely aware of, are not cheap, and can be really challenging when dealing with microscopic amounts of material only.
Summarising:
We have the impression that the reviewers were irritated by our interpretation of the tubular structures we found. We made this interpretation because we thought reviewers would even be more irritated by a mere description of unknown features, without any attempt at interpretation. Our main concern is to bring these unknown features to the attention of the scientific community to hear if, with our combined experience, there are scientists who do know these features, or know in which direction to search. Further detailed analyses as proposed by the reviewers should be attempted, but we believe the first step is to publish the geometry and overall properties of an unknown phenomenon.
Citation: https://doi.org/10.5194/bg-2023-32-AC1
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AC1: 'Reply on RC1', Cees Passchier, 15 May 2023
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RC2: 'Comment on bg-2023-32', Anonymous Referee #2, 01 May 2023
This manuscript presents an interesting observation of the tubular structures found in metamorphic rocks in Namibia and Oman in similar arid desert areas. The tubular structures are partially laminated, located along rock fractures, and surfaced after erosion. In the fresh outcrops, the tubular structures were filled with calcite and depleted on some metals. The authors applied Laser Ablation-Inductively Coupled Plasma Mass Spectrometry, Electron Microprobe Analysis and fluorescence microscopy as imaging techniques to analyze the structures.
The authors observed enrichment in P and S at the rim of some filling and the depletion of Sr, Mn, Fe and some Rare Earth elements (Nd, Th, Ce, Pr, La) in the white materials.
The authors speculated on the "biological" nature of the observed structures. However, no evidence supports the conceptual model (Figure 10). No one technique has been applied to prove the organic origin of P and S in the tubular structures. P and S can also be part of minerals, and autofluorescence signals can be emitted from minerals.
It is also not feasible that water entering fractures will create equidistant distances between tubular, and it is also speculative that microbial cells growing there remain P and S and leave calcite. The authors also suggested that "In addition to growth in the longitudinal direction, radial growth would widen the tubule (Fig. 10C), and this requires Ca transport towards the centre of the cavity, where over time a column is formed that fills the tubule". It is unclear how and why Ca will transport to the centre of the cavity, and the suggested mechanism cannot explain the rows of tubular of approximately similar diameter.
The manuscript contains many speculations, e.g., that the microbes may be a monoculture.
Since the manuscript has no evidence for the main statement about the biological origin of the tubules in metamorphic limestone in Namibia and Oman, I do not recommend the manuscript for publication.
The authors need to bring evidence for their statement. For example, the analysis of biomarkers, Raman mapping and isotopic analysis are required to check the chemical structure of organic matter. I suggest applying some high spatial resolution techniques to support the microbial origin. , e.g., Nano-SIMS.Citation: https://doi.org/10.5194/bg-2023-32-RC2 -
AC2: 'Reply on RC2', Cees Passchier, 15 May 2023
We thank the reviewers for their comments. We appreciate their concerns, but we feel that the most important message of our manuscript has somehow not reached them, namely that no known geological process can explain the observations we describe in our manuscript.
Two of the authors are highly experienced geologists with many years of field experience, and are specialists in metamorphic rocks (JU and CWP). Of course, the authors are aware that fluorescence can be caused by crystalline material (a speciality of author AJ), and that trace elements of S or P can be present in carbonates (something NG and RM-K are also highly familiar with). But what is crucial here is that pores or tubules that form inside a carbonate rock similar to what we described have apparently never before been described. We cannot think of any geological process that can describe the formation of the presented tubules, hence we proposed a biological origin. The structures are apparently fossils, which may or may not still contain recognisable organic material.
The reviewers are correct that the evidence is not conclusive. But we consider this descriptive manuscript as a start, to clearly describe and present the observations. In addition, these must then be interpreted, which is what we did here. Only then can funding be applied for, after which more elaborate and expensive methodology can be used to elucidate the proposed biological origin. We consider this an opportunity that might open a completely novel research subject, and we wish to share our observations with the scientific community. It is a bit of a disappointment that the two reviewers would not allow such an opportunity. One can only imagine what the outcome of a grant review process would be, if we were to apply for money to further investigate this, without any evidence that the observations have been shared with the scientific community. As such, we think it important that our basic geometric observations are published, in order to give other scientists a chance to react and open a discussion what these structures could be.
Below, we address the points raised in more detail.
Reviewer 1:
The authors describe a special type of caliche-calcrete crust, which is often found in hot arid, desert-like areas. These crusts are partially laminated (partly "endostromatolites" whatever this means) with tubular hollow structures up to several centimeters long found on bedrock carbonate surfaces. These structures are probably solution structures caused by organisms that have massively dissolved underlying bedrock carbonate layers. Some of the tube-cavities have been already backfilled or cemented. The cement crusts are enriched in certain elements that were originally enriched in the bedrock carbonate layers. The authors observed enrichments of P and S in some areas and interpret these element enrichments as a biosignature. They also observed autofluorescence in some the special caliche cement crusts, which they attribute to organic material incorporated in the carbonates. The age of the caliche is not known, but could be carried out using 14C and/or other methods. Presumably they are Quaternary formations especially formed during humid climatic phases.
AU response: endostromatolites are mentioned in the reference list. In view of the age of the investigated rocks, 14C dating is difficult because of the large amount of "dead carbon" present in the marble, which would swamp any attempt at dating; we do not see a way to separate the marble from any organic carbon that may be present. In any case, any biological material is most likely fossilized and present in minute amounts, for which the aging methods are not sensitive enough. Also, dating will not solve the riddle of how the observed tubules were formed.
The concept of a “new” biological niche without providing any evidence of life is very optimistic and in this form not acceptable.
AU response: we may have been bold in proposing an entirely new lifeform: what we propose is that we see unexplained structures which are probably of biological origin, and for which we give a tentative explanation. As stated above, an explanation must be given how the observed cavities were formed, and a geological, abiotic explanation is not available. That we propose this as a biological niche is simply in lack of a more plausible explanation not involving micro-organisms. We could be less bold in our manuscript and just ask a simple question: does any specialist in calcrete/carbonate studies who works in deserts know these kinds of structures? Have they ever been described before? Are there specialised labs who would like to further investigate them? But a manuscript only presenting questions and not giving a possible explanation, how unlikely (in the eyes of some) it be, is not providing much progress either. Therefore, we decided to include a description of how these pores and tubules might have formed.
The manuscript has considerable methodological deficiencies. If it is claimed that microorganisms that have produced these caliche tube structure-microbialites, it is imperative that the possibilities of modern bio-geochemical analyses be applied to test this assumption. Following analytical procedures should be used and tested:
1: Raman spectroscopy to test mineral inventory and organic carbon content in the carbonate minerals in caliche and bedrock
AU response: we have applied RAMAN, and although the fluorescence is very strong in the samples, hampering the analysis, we see evidence of elemental C being present, which may be interpreted as fossilized organic material. We can incorporate this in a revised manuscript, but we are not sure this would convince the reviewer.
2: Application of geo-histological techniques (histochemical staining procedures for organic residues).
AU response: Histochemical staining is overly optimistic, as the fossilized organic material is most likely completely decomposed.
3: Stable C-O-S isotope analyses of caliche carbonates und bedrock carbonates to detect possible metabolic fractionation in caliche and bedrock.
AU response: One of the authors (CWP) is a specialist on stable C/O isotope analysis in carbonates and from experience can say that far more material is required for any outcome by this kind of analysis than the tubules can produce. The tubules are very small and only affect a small band in the marbles – any material left behind would be of microscopic quantity only.
4: Lipid biomarker analyses of caliche rocks looking for prokaryote (bacteria + archaea) and eukaryote (e.g. fungi!-lichens) organism traces.
AU response: Again, it is highly unlikely to find lipid biomarkers in these ancient, fossilized rocks.
Autofluorescence effects can also be produced by certain minerals and not necessarily by organic molecules only. Authors must check the literature
AU response: The authors are very much aware of autofluorescence and based on many, many years of experience, we can assure the reviewer that this is not behind the observations. Fluorescent minerals never form tubules, and never form the growth-layer structure on a microscopic scale as we have observed and described here.
The manuscript is not publishable in its present form. The authors have to prove which organism groups were likely involved in the formation of these structures. Probably lichen communities may have played a significant role. The analytical possibilities mentioned above open up possibilities of a comprehensible interpretation.
AU response: It is interesting that on the one hand the reviewer is reluctant to accept a biological origin, and on the other hand proposes that ‘lichen communities [probably] may have played a significant role’. The key point here is that we propose a model how microbiological activity (which we don’t want to pin down on fungi, lichen, archaea or bacteria) can form cavities that are visible by naked eye. That we don’t know which life form was responsible for the formation of these cavities doesn’t mean one can’t speculate that a life form was responsible. If we were to only present the observations without any explanation, simply describing a geometry and asking the question - what is this? (biotic or abiotic), a reviewer would most likely demand an explanation.
Reviewer 2.
This manuscript presents an interesting observation of the tubular structures found in metamorphic rocks in Namibia and Oman in similar arid desert areas. The tubular structures are partially laminated, located along rock fractures, and surfaced after erosion. In the fresh outcrops, the tubular structures were filled with calcite and depleted on some metals. The authors applied Laser Ablation-Inductively Coupled Plasma Mass Spectrometry, Electron Microprobe Analysis and fluorescence microscopy as imaging techniques to analyze the structures.
The authors observed enrichment in P and S at the rim of some filling and the depletion of Sr, Mn, Fe and some Rare Earth elements (Nd, Th, Ce, Pr, La) in the white materials.
The authors speculated on the "biological" nature of the observed structures. However, no evidence supports the conceptual model (Figure 10). No one technique has been applied to prove the organic origin of P and S in the tubular structures. P and S can also be part of minerals, and autofluorescence signals can be emitted from minerals.AU response: as stated above, describing the observations without any possible explanation how they arose (as unlikely as the explanation may seem) is not very satisfactory. A conceptual model was proposed to explain how macroscopic structures can be formed by microscopic organisms. The authors are aware that P and S can be ‘part of minerals’ and that minerals can cause autofluorescence. That is not what we see here, a statement that is based on years of experience in carbonate microscopy. No known mineral spontaneously grows in the shapes we have observed and described here.
It is also not feasible that water entering fractures will create equidistant distances between tubular, and it is also speculative that microbial cells growing there remain P and S and leave calcite. The authors also suggested that "In addition to growth in the longitudinal direction, radial growth would widen the tubule (Fig. 10C), and this requires Ca transport towards the centre of the cavity, where over time a column is formed that fills the tubule". It is unclear how and why Ca will transport to the centre of the cavity, and the suggested mechanism cannot explain the rows of tubular of approximately similar diameter.
AU response: The equidistant position of the tubules was not the result of water entering fractures, but may have been caused by nutrient competition of starting communities. That Ca transport is needed towards the centre is a result of how the hypothesized community would grow: it starts at the centre, but grows radially out of this centre. In order to make space, material that can’t be incorporated into biomatter (here, Ca) must be deposited, which can be done at the centre, where growth is no longer possible, as all nutrients have been used. A single layer of microorganisms wouldn’t require much Ca transport, but would not produce pores that are macroscopically visible.
The manuscript contains many speculations, e.g., that the microbes may be a monoculture.AU response: Either microbes are a monoculture or they are a complex community. We tried to start with the simplest possibility, that of a monoculture. Of course, a more complex community is also possible, in which case multiple species would have to reach the niche simultaneously or sequentially.
Since the manuscript has no evidence for the main statement about the biological origin of the tubules in metamorphic limestone in Namibia and Oman, I do not recommend the manuscript for publication.AU response: This boils down to what we state at the beginning of this letter: there is simply no geological explanation for these tubules. This is a completely novel observation, though it is not unique to one rock or one location. Sometimes, a novelty is just that: something not yet described. And what authors are supposed to do in that case is clearly describe what they observe, and interpret their findings as best as they can. We accept that our explanation is speculative, but again, no other explanation can be given (not by us, and apparently also not by the reviewers).
The authors need to bring evidence for their statement. For example, the analysis of biomarkers, Raman mapping and isotopic analysis are required to check the chemical structure of organic matter. I suggest applying some high spatial resolution techniques to support the microbial origin. , e.g., Nano-SIMS.AU response: Once our findings are published, one can start to consider applying for grants to investigate this further, or collaborate with others who have the facilities and interest to do so. Without a publication, there is no chance that we, or others (and we are happy to share our rock samples with other scientists) can raise funding for further analyses, which, as this reviewer is surely aware of, are not cheap, and can be really challenging when dealing with microscopic amounts of material only.
Summarising:
We have the impression that the reviewers were irritated by our interpretation of the tubular structures we found. We propose this interpretation because we thought reviewers would even be more irritated by a mere description of unknown features, without any attempt at interpretation. Our main concern is to bring these unknown features to the attention of the scientific community to hear if, with our combined experience, there are scientists who do know these features, or know in which direction to further research them. More detailed analyses as proposed by the reviewers should be attempted, but we believe the first step is to publish the geometry and overall properties of this unknown and novel phenomenon.
Citation: https://doi.org/10.5194/bg-2023-32-AC2
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AC2: 'Reply on RC2', Cees Passchier, 15 May 2023
Status: closed
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RC1: 'Comment on bg-2023-32', Anonymous Referee #1, 29 Mar 2023
The authors describe a special type of caliche-calcrete crust, which is often found in hot arid, desert-like areas. These crusts are partially laminated (partly "endostromatolites" whatever this means) with tubular hollow structures up to several centimeters long found on bedrock carbonate surfaces. These structures are probably solution structures caused by organisms that have massively dissolved underlying bedrock carbonate layers. Some of the tube-cavities have been already backfilled or cemented. The cement crusts are enriched in certain elements that were originally enriched in the bedrock carbonate layers. The authors observed enrichments of P and S in some areas and interpret these element enrichments as a biosignature. They also observed autofluorescence in some the special caliche cement crusts, which they attribute to organic material incorporated in the carbonates. The age of the caliche is not known, but could be carried out using 14C and/or other methods. Presumably they are Quaternary formations especially formed during humid climatic phases.
The concept of a “new” biological niche without providing any evidence of life is very optimistic and in this form not acceptable. The manuscript has considerable methodological deficiencies. If it is claimed that microorganisms that have produced these caliche tube structure-microbialites, it is imperative that the possibilities of modern bio-geochemical analyses be applied to test this assumption. Following analytical procedures should be used and tested:
1: Raman spectroscopy to test mineral inventory and organic carbon content in the carbonate minerals in caliche and bedrock
2: Application of geo-histological techniques (histochemical staining procedures for organic residues).
3: Stable C-O-S isotope analyses of caliche carbonates und bedrock carbonates to detect possible metabolic fractionation in caliche and bedrock.
4: Lipid biomarker analyses of caliche rocks looking for prokaryote (bacteria + archaea) and eukaryote (e.g. fungi!-lichens) organism traces.
Autofluorescence effects can also be produced by certain minerals and not necessarily by organic molecules only. Authors must check the literature
The manuscript is not publishable in its present form. The authors have to prove which organism groups were likely involved in the formation of these structures. Probably lichen communities may have played a significant role. The analytical possibilities mentioned above open up possibilities of a comprehensible interpretation.
Citation: https://doi.org/10.5194/bg-2023-32-RC1 -
AC1: 'Reply on RC1', Cees Passchier, 15 May 2023
We thank the reviewers for their comments. We appreciate their concerns, but we feel that the most important message of our manuscript has somehow not reached them, namely that no known geological process can explain the observations we describe in our manuscript.
Two of the authors are highly experienced geologists with many years of field experience, and are specialists in metamorphic rocks (JU and CWP). Of course, the authors are aware that fluorescence can be caused by crystalline material (a speciality of author AJ), and that trace elements of S or P can be present in carbonates (something NG and RM-K are also highly familiar with). But what is crucial here is that pores or tubules that form inside a carbonate rock similar to what we described have apparently never before been described. We cannot think of any geological process that can describe the formation of the presented tubules, hence we proposed a biological origin. The structures are apparently fossils, which may or may not still contain recognisable organic material.
The reviewers are correct that the evidence is not conclusive. But we consider this descriptive manuscript as a start, to clearly describe and present the observations. In addition, these must then be interpreted, which is what we did here. Only then can funding be applied for, after which more elaborate and expensive methodology can be used to elucidate the proposed biological origin. We consider this an opportunity that might open a completely novel research subject, and we wish to share our observations with the scientific community. It is a bit of a disappointment that the two reviewers would not allow such an opportunity. One can only imagine what the outcome of a grant review process would be, if we were to apply for money to further investigate this, without any evidence that the observations have been shared with the scientific community. As such, we think it important that our basic geometric observations are published, in order to give other scientists a chance to react and open a discussion what these structures could be.
Below, we address the points raised in more detail.
Reviewer 1:
The authors describe a special type of caliche-calcrete crust, which is often found in hot arid, desert-like areas. These crusts are partially laminated (partly "endostromatolites" whatever this means) with tubular hollow structures up to several centimeters long found on bedrock carbonate surfaces. These structures are probably solution structures caused by organisms that have massively dissolved underlying bedrock carbonate layers. Some of the tube-cavities have been already backfilled or cemented. The cement crusts are enriched in certain elements that were originally enriched in the bedrock carbonate layers. The authors observed enrichments of P and S in some areas and interpret these element enrichments as a biosignature. They also observed autofluorescence in some the special caliche cement crusts, which they attribute to organic material incorporated in the carbonates. The age of the caliche is not known, but could be carried out using 14C and/or other methods. Presumably they are Quaternary formations especially formed during humid climatic phases.
AU response: endostromatolites are mentioned in the reference list. In view of the age of the investigated rocks, 14C dating is difficult because of the large amount of "dead carbon" present in the marble, which would swamp any attempt at dating; we do not see a way to separate the marble from any organic carbon that may be present. In any case, any biological material is most likely fossilized and present in minute amounts, for which the aging methods are not sensitive enough. Also, dating will not solve the riddle of how the observed tubules were formed.
The concept of a “new” biological niche without providing any evidence of life is very optimistic and in this form not acceptable.
AU response: we may have been bold in proposing an entirely new lifeform: what we propose is that we see unexplained structures which are probably of biological origin, and for which we give a tentative explanation. As stated above, an explanation must be given how the observed cavities were formed, and a geological, abiotic explanation is not available. That we propose this as a biological niche is simply in lack of a more plausible explanation not involving micro-organisms. We could be less bold in our manuscript and just ask a simple question: does any specialist in calcrete/carbonate studies who works in deserts know these kinds of structures? Have they ever been described before? Are there specialised labs who would like to further investigate them? But a manuscript only presenting questions and not giving a possible explanation, how unlikely (in the eyes of some) it be, is not providing much progress either. Therefore, we decided to include a description of how these pores and tubules might have formed.
The manuscript has considerable methodological deficiencies. If it is claimed that microorganisms that have produced these caliche tube structure-microbialites, it is imperative that the possibilities of modern bio-geochemical analyses be applied to test this assumption. Following analytical procedures should be used and tested:
1: Raman spectroscopy to test mineral inventory and organic carbon content in the carbonate minerals in caliche and bedrock
AU response: we have applied RAMAN, and although the fluorescence is very strong in the samples, hampering the analysis, we see evidence of elemental C being present, which may be interpreted as fossilized organic material. We can incorporate this in a revised manuscript, but we are not sure this would convince the reviewer.
2: Application of geo-histological techniques (histochemical staining procedures for organic residues).
AU response: Histochemical staining is overly optimistic, as the fossilized organic material is most likely completely decomposed.
3: Stable C-O-S isotope analyses of caliche carbonates und bedrock carbonates to detect possible metabolic fractionation in caliche and bedrock.
AU response: One of the authors (CWP) is a specialist on stable C/O isotope analysis in carbonates and from experience can say that far more material is required for any outcome by this kind of analysis than the tubules can produce. The tubules are very small and only affect a small band in the marbles – any material left behind would be of microscopic quantity only.
4: Lipid biomarker analyses of caliche rocks looking for prokaryote (bacteria + archaea) and eukaryote (e.g. fungi!-lichens) organism traces.
AU response: Again, it is highly unlikely to find lipid biomarkers in these ancient, fossilized rocks.
Autofluorescence effects can also be produced by certain minerals and not necessarily by organic molecules only. Authors must check the literature
AU response: The authors are very much aware of autofluorescence and based on many, many years of experience, we can assure the reviewer that this is not behind the observations. Fluorescent minerals never form tubules, and never form the growth-layer structure on a microscopic scale as we have observed and described here.
The manuscript is not publishable in its present form. The authors have to prove which organism groups were likely involved in the formation of these structures. Probably lichen communities may have played a significant role. The analytical possibilities mentioned above open up possibilities of a comprehensible interpretation.
AU response: It is interesting that on the one hand the reviewer is reluctant to accept a biological origin, and on the other hand proposes that ‘lichen communities [probably] may have played a significant role’. The key point here is that we propose a model how microbiological activity (which we don’t want to pin down on fungi, lichen, archaea or bacteria) can form cavities that are visible by naked eye. That we don’t know which life form was responsible for the formation of these cavities doesn’t mean one can’t speculate that a life form was responsible. If we were to only present the observations without any explanation, simply describing a geometry and asking the question - what is this? (biotic or abiotic), a reviewer would most likely demand an explanation.
Reviewer 2.
This manuscript presents an interesting observation of the tubular structures found in metamorphic rocks in Namibia and Oman in similar arid desert areas. The tubular structures are partially laminated, located along rock fractures, and surfaced after erosion. In the fresh outcrops, the tubular structures were filled with calcite and depleted on some metals. The authors applied Laser Ablation-Inductively Coupled Plasma Mass Spectrometry, Electron Microprobe Analysis and fluorescence microscopy as imaging techniques to analyze the structures.
The authors observed enrichment in P and S at the rim of some filling and the depletion of Sr, Mn, Fe and some Rare Earth elements (Nd, Th, Ce, Pr, La) in the white materials.
The authors speculated on the "biological" nature of the observed structures. However, no evidence supports the conceptual model (Figure 10). No one technique has been applied to prove the organic origin of P and S in the tubular structures. P and S can also be part of minerals, and autofluorescence signals can be emitted from minerals.AU response: as stated above, describing the observations without any possible explanation how they arose (as unlikely as the explanation may seem) is not very satisfactory. A conceptual model was proposed to explain how macroscopic structures can be formed by microscopic organisms. The authors are aware that P and S can be ‘part of minerals’ and that minerals can cause autofluorescence. That is not what we see here, a statement that is based on years of experience in carbonate microscopy. No known mineral spontaneously grows in the shapes we have observed and described here.
It is also not feasible that water entering fractures will create equidistant distances between tubular, and it is also speculative that microbial cells growing there remain P and S and leave calcite. The authors also suggested that "In addition to growth in the longitudinal direction, radial growth would widen the tubule (Fig. 10C), and this requires Ca transport towards the centre of the cavity, where over time a column is formed that fills the tubule". It is unclear how and why Ca will transport to the centre of the cavity, and the suggested mechanism cannot explain the rows of tubular of approximately similar diameter.
AU response: The equidistant position of the tubules was not the result of water entering fractures, but may have been caused by nutrient competition of starting communities. That Ca transport is needed towards the centre is a result of how the hypothesized community would grow: it starts at the centre, but grows radially out of this centre. In order to make space, material that can’t be incorporated into biomatter (here, Ca) must be deposited, which can be done at the centre, where growth is no longer possible, as all nutrients have been used. A single layer of microorganisms wouldn’t require much Ca transport, but would not produce pores that are macroscopically visible.
The manuscript contains many speculations, e.g., that the microbes may be a monoculture.AU response: Either microbes are a monoculture or they are a complex community. We tried to start with the simplest possibility, that of a monoculture. Of course, a more complex community is also possible, in which case multiple species would have to reach the niche simultaneously or sequentially.
Since the manuscript has no evidence for the main statement about the biological origin of the tubules in metamorphic limestone in Namibia and Oman, I do not recommend the manuscript for publication.AU response: This boils down to what we state at the beginning of this letter: there is simply no geological explanation for these tubules. This is a completely novel observation, though it is not unique to one rock or one location. Sometimes, a novelty is just that: something not yet described. And what authors are supposed to do in that case is clearly describe what they observe, and interpret their findings as best as they can. We accept that our explanation is speculative, but again, no other explanation can be given (not by us, and apparently also not by the reviewers).
The authors need to bring evidence for their statement. For example, the analysis of biomarkers, Raman mapping and isotopic analysis are required to check the chemical structure of organic matter. I suggest applying some high spatial resolution techniques to support the microbial origin. , e.g., Nano-SIMS.AU response: Once our findings are published, one can start to consider applying for grants to investigate this further, or collaborate with others who have the facilities and interest to do so. Without a publication, there is no chance that we, or others (and we are happy to share our rock samples with other scientists) can raise funding for further analyses, which, as this reviewer is surely aware of, are not cheap, and can be really challenging when dealing with microscopic amounts of material only.
Summarising:
We have the impression that the reviewers were irritated by our interpretation of the tubular structures we found. We propose this interpretation because we thought reviewers would even be more irritated by a mere description of unknown features, without any attempt at interpretation. Our main concern is to bring these unknown features to the attention of the scientific community to hear if, with our combined experience, there are scientists who do know these features, or know in which direction to further research them. More detailed analyses as proposed by the reviewers should be attempted, but we believe the first step is to publish the geometry and overall properties of this unknown and novel phenomenon.
Since the manuscript has no evidence for the main statement about the biological origin of the tubules in metamorphic limestone in Namibia and Oman, I do not recommend the manuscript for publication.AU response: This boils down to what we state at the beginning of this letter: there is simply no geological explanation for these tubules. This is a completely novel observation, though it is not unique to one rock or one location. Sometimes, a novelty is just that: something not yet described. And what authors are supposed to do in that case is clearly describe what they observe, and interpret their findings as best as they can. We accept that our explanation is speculative, but again, no other explanation can be given (not by us, and apparently also not by the reviewers).
The authors need to bring evidence for their statement. For example, the analysis of biomarkers, Raman mapping and isotopic analysis are required to check the chemical structure of organic matter. I suggest applying some high spatial resolution techniques to support the microbial origin. , e.g., Nano-SIMS.AU response: Once our findings are published, one can start to consider applying for grants to investigate this further, or collaborate with others who have the facilities and interest to do so. Without a publication, there is no chance that we, or others (and we are happy to share our rock samples with other scientists) can raise funding for further analyses, which, as this reviewer is surely aware of, are not cheap, and can be really challenging when dealing with microscopic amounts of material only.
Summarising:
We have the impression that the reviewers were irritated by our interpretation of the tubular structures we found. We made this interpretation because we thought reviewers would even be more irritated by a mere description of unknown features, without any attempt at interpretation. Our main concern is to bring these unknown features to the attention of the scientific community to hear if, with our combined experience, there are scientists who do know these features, or know in which direction to search. Further detailed analyses as proposed by the reviewers should be attempted, but we believe the first step is to publish the geometry and overall properties of an unknown phenomenon.
Citation: https://doi.org/10.5194/bg-2023-32-AC1
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AC1: 'Reply on RC1', Cees Passchier, 15 May 2023
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RC2: 'Comment on bg-2023-32', Anonymous Referee #2, 01 May 2023
This manuscript presents an interesting observation of the tubular structures found in metamorphic rocks in Namibia and Oman in similar arid desert areas. The tubular structures are partially laminated, located along rock fractures, and surfaced after erosion. In the fresh outcrops, the tubular structures were filled with calcite and depleted on some metals. The authors applied Laser Ablation-Inductively Coupled Plasma Mass Spectrometry, Electron Microprobe Analysis and fluorescence microscopy as imaging techniques to analyze the structures.
The authors observed enrichment in P and S at the rim of some filling and the depletion of Sr, Mn, Fe and some Rare Earth elements (Nd, Th, Ce, Pr, La) in the white materials.
The authors speculated on the "biological" nature of the observed structures. However, no evidence supports the conceptual model (Figure 10). No one technique has been applied to prove the organic origin of P and S in the tubular structures. P and S can also be part of minerals, and autofluorescence signals can be emitted from minerals.
It is also not feasible that water entering fractures will create equidistant distances between tubular, and it is also speculative that microbial cells growing there remain P and S and leave calcite. The authors also suggested that "In addition to growth in the longitudinal direction, radial growth would widen the tubule (Fig. 10C), and this requires Ca transport towards the centre of the cavity, where over time a column is formed that fills the tubule". It is unclear how and why Ca will transport to the centre of the cavity, and the suggested mechanism cannot explain the rows of tubular of approximately similar diameter.
The manuscript contains many speculations, e.g., that the microbes may be a monoculture.
Since the manuscript has no evidence for the main statement about the biological origin of the tubules in metamorphic limestone in Namibia and Oman, I do not recommend the manuscript for publication.
The authors need to bring evidence for their statement. For example, the analysis of biomarkers, Raman mapping and isotopic analysis are required to check the chemical structure of organic matter. I suggest applying some high spatial resolution techniques to support the microbial origin. , e.g., Nano-SIMS.Citation: https://doi.org/10.5194/bg-2023-32-RC2 -
AC2: 'Reply on RC2', Cees Passchier, 15 May 2023
We thank the reviewers for their comments. We appreciate their concerns, but we feel that the most important message of our manuscript has somehow not reached them, namely that no known geological process can explain the observations we describe in our manuscript.
Two of the authors are highly experienced geologists with many years of field experience, and are specialists in metamorphic rocks (JU and CWP). Of course, the authors are aware that fluorescence can be caused by crystalline material (a speciality of author AJ), and that trace elements of S or P can be present in carbonates (something NG and RM-K are also highly familiar with). But what is crucial here is that pores or tubules that form inside a carbonate rock similar to what we described have apparently never before been described. We cannot think of any geological process that can describe the formation of the presented tubules, hence we proposed a biological origin. The structures are apparently fossils, which may or may not still contain recognisable organic material.
The reviewers are correct that the evidence is not conclusive. But we consider this descriptive manuscript as a start, to clearly describe and present the observations. In addition, these must then be interpreted, which is what we did here. Only then can funding be applied for, after which more elaborate and expensive methodology can be used to elucidate the proposed biological origin. We consider this an opportunity that might open a completely novel research subject, and we wish to share our observations with the scientific community. It is a bit of a disappointment that the two reviewers would not allow such an opportunity. One can only imagine what the outcome of a grant review process would be, if we were to apply for money to further investigate this, without any evidence that the observations have been shared with the scientific community. As such, we think it important that our basic geometric observations are published, in order to give other scientists a chance to react and open a discussion what these structures could be.
Below, we address the points raised in more detail.
Reviewer 1:
The authors describe a special type of caliche-calcrete crust, which is often found in hot arid, desert-like areas. These crusts are partially laminated (partly "endostromatolites" whatever this means) with tubular hollow structures up to several centimeters long found on bedrock carbonate surfaces. These structures are probably solution structures caused by organisms that have massively dissolved underlying bedrock carbonate layers. Some of the tube-cavities have been already backfilled or cemented. The cement crusts are enriched in certain elements that were originally enriched in the bedrock carbonate layers. The authors observed enrichments of P and S in some areas and interpret these element enrichments as a biosignature. They also observed autofluorescence in some the special caliche cement crusts, which they attribute to organic material incorporated in the carbonates. The age of the caliche is not known, but could be carried out using 14C and/or other methods. Presumably they are Quaternary formations especially formed during humid climatic phases.
AU response: endostromatolites are mentioned in the reference list. In view of the age of the investigated rocks, 14C dating is difficult because of the large amount of "dead carbon" present in the marble, which would swamp any attempt at dating; we do not see a way to separate the marble from any organic carbon that may be present. In any case, any biological material is most likely fossilized and present in minute amounts, for which the aging methods are not sensitive enough. Also, dating will not solve the riddle of how the observed tubules were formed.
The concept of a “new” biological niche without providing any evidence of life is very optimistic and in this form not acceptable.
AU response: we may have been bold in proposing an entirely new lifeform: what we propose is that we see unexplained structures which are probably of biological origin, and for which we give a tentative explanation. As stated above, an explanation must be given how the observed cavities were formed, and a geological, abiotic explanation is not available. That we propose this as a biological niche is simply in lack of a more plausible explanation not involving micro-organisms. We could be less bold in our manuscript and just ask a simple question: does any specialist in calcrete/carbonate studies who works in deserts know these kinds of structures? Have they ever been described before? Are there specialised labs who would like to further investigate them? But a manuscript only presenting questions and not giving a possible explanation, how unlikely (in the eyes of some) it be, is not providing much progress either. Therefore, we decided to include a description of how these pores and tubules might have formed.
The manuscript has considerable methodological deficiencies. If it is claimed that microorganisms that have produced these caliche tube structure-microbialites, it is imperative that the possibilities of modern bio-geochemical analyses be applied to test this assumption. Following analytical procedures should be used and tested:
1: Raman spectroscopy to test mineral inventory and organic carbon content in the carbonate minerals in caliche and bedrock
AU response: we have applied RAMAN, and although the fluorescence is very strong in the samples, hampering the analysis, we see evidence of elemental C being present, which may be interpreted as fossilized organic material. We can incorporate this in a revised manuscript, but we are not sure this would convince the reviewer.
2: Application of geo-histological techniques (histochemical staining procedures for organic residues).
AU response: Histochemical staining is overly optimistic, as the fossilized organic material is most likely completely decomposed.
3: Stable C-O-S isotope analyses of caliche carbonates und bedrock carbonates to detect possible metabolic fractionation in caliche and bedrock.
AU response: One of the authors (CWP) is a specialist on stable C/O isotope analysis in carbonates and from experience can say that far more material is required for any outcome by this kind of analysis than the tubules can produce. The tubules are very small and only affect a small band in the marbles – any material left behind would be of microscopic quantity only.
4: Lipid biomarker analyses of caliche rocks looking for prokaryote (bacteria + archaea) and eukaryote (e.g. fungi!-lichens) organism traces.
AU response: Again, it is highly unlikely to find lipid biomarkers in these ancient, fossilized rocks.
Autofluorescence effects can also be produced by certain minerals and not necessarily by organic molecules only. Authors must check the literature
AU response: The authors are very much aware of autofluorescence and based on many, many years of experience, we can assure the reviewer that this is not behind the observations. Fluorescent minerals never form tubules, and never form the growth-layer structure on a microscopic scale as we have observed and described here.
The manuscript is not publishable in its present form. The authors have to prove which organism groups were likely involved in the formation of these structures. Probably lichen communities may have played a significant role. The analytical possibilities mentioned above open up possibilities of a comprehensible interpretation.
AU response: It is interesting that on the one hand the reviewer is reluctant to accept a biological origin, and on the other hand proposes that ‘lichen communities [probably] may have played a significant role’. The key point here is that we propose a model how microbiological activity (which we don’t want to pin down on fungi, lichen, archaea or bacteria) can form cavities that are visible by naked eye. That we don’t know which life form was responsible for the formation of these cavities doesn’t mean one can’t speculate that a life form was responsible. If we were to only present the observations without any explanation, simply describing a geometry and asking the question - what is this? (biotic or abiotic), a reviewer would most likely demand an explanation.
Reviewer 2.
This manuscript presents an interesting observation of the tubular structures found in metamorphic rocks in Namibia and Oman in similar arid desert areas. The tubular structures are partially laminated, located along rock fractures, and surfaced after erosion. In the fresh outcrops, the tubular structures were filled with calcite and depleted on some metals. The authors applied Laser Ablation-Inductively Coupled Plasma Mass Spectrometry, Electron Microprobe Analysis and fluorescence microscopy as imaging techniques to analyze the structures.
The authors observed enrichment in P and S at the rim of some filling and the depletion of Sr, Mn, Fe and some Rare Earth elements (Nd, Th, Ce, Pr, La) in the white materials.
The authors speculated on the "biological" nature of the observed structures. However, no evidence supports the conceptual model (Figure 10). No one technique has been applied to prove the organic origin of P and S in the tubular structures. P and S can also be part of minerals, and autofluorescence signals can be emitted from minerals.AU response: as stated above, describing the observations without any possible explanation how they arose (as unlikely as the explanation may seem) is not very satisfactory. A conceptual model was proposed to explain how macroscopic structures can be formed by microscopic organisms. The authors are aware that P and S can be ‘part of minerals’ and that minerals can cause autofluorescence. That is not what we see here, a statement that is based on years of experience in carbonate microscopy. No known mineral spontaneously grows in the shapes we have observed and described here.
It is also not feasible that water entering fractures will create equidistant distances between tubular, and it is also speculative that microbial cells growing there remain P and S and leave calcite. The authors also suggested that "In addition to growth in the longitudinal direction, radial growth would widen the tubule (Fig. 10C), and this requires Ca transport towards the centre of the cavity, where over time a column is formed that fills the tubule". It is unclear how and why Ca will transport to the centre of the cavity, and the suggested mechanism cannot explain the rows of tubular of approximately similar diameter.
AU response: The equidistant position of the tubules was not the result of water entering fractures, but may have been caused by nutrient competition of starting communities. That Ca transport is needed towards the centre is a result of how the hypothesized community would grow: it starts at the centre, but grows radially out of this centre. In order to make space, material that can’t be incorporated into biomatter (here, Ca) must be deposited, which can be done at the centre, where growth is no longer possible, as all nutrients have been used. A single layer of microorganisms wouldn’t require much Ca transport, but would not produce pores that are macroscopically visible.
The manuscript contains many speculations, e.g., that the microbes may be a monoculture.AU response: Either microbes are a monoculture or they are a complex community. We tried to start with the simplest possibility, that of a monoculture. Of course, a more complex community is also possible, in which case multiple species would have to reach the niche simultaneously or sequentially.
Since the manuscript has no evidence for the main statement about the biological origin of the tubules in metamorphic limestone in Namibia and Oman, I do not recommend the manuscript for publication.AU response: This boils down to what we state at the beginning of this letter: there is simply no geological explanation for these tubules. This is a completely novel observation, though it is not unique to one rock or one location. Sometimes, a novelty is just that: something not yet described. And what authors are supposed to do in that case is clearly describe what they observe, and interpret their findings as best as they can. We accept that our explanation is speculative, but again, no other explanation can be given (not by us, and apparently also not by the reviewers).
The authors need to bring evidence for their statement. For example, the analysis of biomarkers, Raman mapping and isotopic analysis are required to check the chemical structure of organic matter. I suggest applying some high spatial resolution techniques to support the microbial origin. , e.g., Nano-SIMS.AU response: Once our findings are published, one can start to consider applying for grants to investigate this further, or collaborate with others who have the facilities and interest to do so. Without a publication, there is no chance that we, or others (and we are happy to share our rock samples with other scientists) can raise funding for further analyses, which, as this reviewer is surely aware of, are not cheap, and can be really challenging when dealing with microscopic amounts of material only.
Summarising:
We have the impression that the reviewers were irritated by our interpretation of the tubular structures we found. We propose this interpretation because we thought reviewers would even be more irritated by a mere description of unknown features, without any attempt at interpretation. Our main concern is to bring these unknown features to the attention of the scientific community to hear if, with our combined experience, there are scientists who do know these features, or know in which direction to further research them. More detailed analyses as proposed by the reviewers should be attempted, but we believe the first step is to publish the geometry and overall properties of this unknown and novel phenomenon.
Citation: https://doi.org/10.5194/bg-2023-32-AC2
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AC2: 'Reply on RC2', Cees Passchier, 15 May 2023
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