Fractionation of stable carbon isotopes during formate consumption in anoxic rice paddy soils and lake sediments

Conrad, Ralf; Claus, Peter

doi:https://doi.org/10.5194/egusphere-2023-2279

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https://doi.org/10.5194/egusphere-2023-2279

Preprints

03 Nov 2023

| 03 Nov 2023

Fractionation of stable carbon isotopes during formate consumption in anoxic rice paddy soils and lake sediments

Ralf Conrad and Peter Claus

Abstract. Formate is energetically equivalent to hydrogen and thus, is an important intermediate during the breakdown of organic matter in anoxic rice paddy soils and lake sediments. Formate is a common substrate for methanogenesis, homoacetogenesis and sulfate reduction. However, how much these processes contribute to formate degradation and fractionate carbon stable isotopes is largely unknown. Therefore, we measured the conversion of formate to acetate, CH₄ and CO₂ and the δ¹³C of these compounds in samples of paddy soils from Vercelli (Italy) and the International Rice Research Institute (IRRI, the Philippines) and of sediments from the NE and SW basins of Lake Fuchskuhle (Germany). The samples were suspended in phosphate buffer (pH 7.0) both in the absence and presence of sulfate (gypsum) and of methyl fluoride (CH₃F), an inhibitor of aceticlastic methanogenesis. In the paddy soils, formate was mainly converted to acetate both under methanogenic and sulfidogenic conditions. Methane was only a minor product and was mainly formed from the acetate. In the lake sediments, the product spectrum was similar, but only under methanogenic conditions. In the presence of sulfate, however, acetate and CH₄ were only minor products. The isotopic enrichment factors (ε_form) of formate consumption, determined by Mariotti plots, were in the low range of -8 ‰ to -2.5 ‰ when sulfate was absent and formate was mainly converted to acetate and CH₄. However, no enrichment factor was detectable when formate was degraded with sulfate to mainly CO₂. The δ¹³C of acetate was by about 25–50 ‰ more negative than that of formate indicating acetate production by chemolithotrophic homoacetogenesis. Hence, formate seems to be an excellent substrate for homoacetogenesis in anoxic soils and sediments, so that this process is competing well with methanogenesis and sulfate reduction.

Received: 06 Oct 2023 – Discussion started: 03 Nov 2023

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11 Mar 2024

Fractionation of stable carbon isotopes during formate consumption in anoxic rice paddy soils and lake sediments

Ralf Conrad and Peter Claus

Biogeosciences, 21, 1161–1172, https://doi.org/10.5194/bg-21-1161-2024,https://doi.org/10.5194/bg-21-1161-2024, 2024

Short summary

Ralf Conrad and Peter Claus

Interactive discussion

Status: closed

RC1:
'Comment on egusphere-2023-2279', Anonymous Referee #1, 10 Nov 2023
In this manuscript, the authors report on carbon isotope fractionation during formate transformation in rice paddy soils and lake sediment. They observe formate utilization mainly through homoacetogenesis to be the dominant process that outcompetes methanogenesis and sulfate reduction.
As it appears, the data were collected and evaluated correctly and there is no doubt on their reliability. Nonetheless, it does not become clear why this study was performed and what the outcome is in some few clear sentences. Why was sediment from Fuchskuhle used? Because there were still some 6 years old sediment samples in the coldroom? What are the properties of this specific (and internationally not so well-known) lake (pH, carbonate and sulfate content, trophic status etc.)? Is it representative of freshwater lakes in general? Which general conclusions can be drawn from this study?
Minor comments:
111, l. 120: Omit “the”

190: Sentence unclear.

Fig. 6, correct Formiat to Formate.
307: Energy cannot be generated.

342: equivalents.

403: Where are the data on the 16SrRNA genes?

404: “composition of these genes”? What do the authors mean with that?

425: …are degraded in these paddy soils…

434: author
Citation: https://doi.org/10.5194/egusphere-2023-2279-RC1
- AC1:
  'Reply on RC1', Ralf Conrad, 11 Nov 2023
  
  The incentive for the study is stated in L74-79: “The ε values of methanogenesis or homoacetogenesis from H2 plus CO2 are large (Blaser and Conrad, 2016). However, our knowledge of carbon isotope fractionation with formate as substrate is scarce. In cultures of homoacetogenic bacteria the carbon in the acetate produced from formate was strongly depleted in 13C (ε = -56.5‰) almost similarly as with CO2 as carbon source (Freude and Blaser, 2016). However, it is not known which enrichment factors operate in methanogenic or sulfidogenic environmental samples.” For this purpose, we arbitrarily chose two different methanogenic environments, paddy soil and Lake Fuchskuhle sediments. The reason for chosing them was simply because we had used them before and had background information (e.g. gene sequences). Of course we could have chosen different environments (sewage digestor, peat), but a priori it did not matter in which samples to test for fractionation factors of formate degradation.
  It was during the study of fractionation factors that we realized that formate degradation was dominated by homoacetogenesis, which we found to be intriguing. I must admit that we initially expected that formate would be mainly consumed by methanogenesis. However, this was not the case. We briefly discussed this observation but did not present a theoretical explanation. Perhaps we should speculate about the different molecular mechanisms of formate utilization in acetogens versus methanogens, such as outlined in the recent review by Lemaire et al. (Frontiers Microbiol. 2020). General conclusions are that homoacetogenesis seems to be a major pathway of formate utilization in nature, and that strong fractionation of carbon isotopes occurs mainly during the formation of acetate via the Wood-Ljungdahl pathway, while the initital consumption of formate displayed only a small enrichment factor.
  Lake Fuchskuhle is a lake in Northern Germany, which had been the subject of several studies, also own ones. We can expand the description. For our purpose it was as good as any other lake.
  By the way, the lake sediment was sampled in 2016, and the experiments were performed in 2017. The experiments on paddy soils were done in 2016. We mentioned that the study of formate degradation was one out of three studies that were performed almost in parallel. The other two studies (quoted in the ms) concerned the degradation and isotope fractionation of acetate and of propionate, both previously published in Biogeosciences.
  
  Citation: https://doi.org/10.5194/egusphere-2023-2279-AC1
  - RC2: 'Reply on AC1', Anonymous Referee #1, 13 Nov 2023
    
    The authors have answered my concerns convincingly.
    
    Citation: https://doi.org/10.5194/egusphere-2023-2279-RC2
    
    AC3: 'Reply on RC2', Ralf Conrad, 22 Dec 2023
    
    Thank you for the comments
    
    Citation: https://doi.org/10.5194/egusphere-2023-2279-AC3
RC3:
'Comment on egusphere-2023-2279', Anonymous Referee #2, 04 Dec 2023

General Comments
The manuscript by Conrad and Claus, entitled "Fractionation of stable carbon isotopes during formate consumption in anoxic rice paddy soils and lake sediments" presents an interesting study that analyzes isotope effects associated with formate consumption during incubation experiments. The experiments were conducted with two rice pady soils and two lake sediments, each in triplicate at an incubation temperature of 25°C and over a period of four weeks. The authors have used a straightforward experimental approach and state-of-the art analytical methods, including stable isotope analyses of methane by GC-IRMS and stable isotope analyses of formate and acetate by HPLC-IRMS. They observe formation of acetate from formate with a strong ¹³C-depletion of acetate relative to formate, pointing to homoacetogenesis via the Wood-Ljungdahl pathway.
The scientific questions are relevant and within the scope of BG. The isotopic data are novel. They are discussed in an appropriate and balanced way, and the conclusion is substantial. I couldn't detect major scientific flaws.
My major scientific concern is the amendment of fairly large amounts of formate that produce starting concentrations of more than 15 mM in the incubation experiments. How do these concentrations compare to natural formate levels in paddy soils, lake sediments or other environments? And would formate still be an excellent substrate for acetate production via homoacetogenesis at natural concentration levels? How valid are the findings at 25°C for lake sediments that are generally much colder under in situ conditions? These questions warrant some further discussion.
The manuscript is well organized overall, but the quality of the figures needs improvement. Clear and concise figure captions and legends could improve the readability of the manuscript a lot.
Specific comments and suggestions for the improvement of figures:
Figure 1: The figure legend is incomplete. The crosses representing the controls are not present. Panels c, d and h display a varying shade of red with no clarification. In my opinion, the size of the axis title font is quite small. While the title of the x-axis is capitalized, that of the y-axis is not. In panel e, f, g, and h, it would be appropriate to add "vs VPDB" to the per mil sign on the y-axis. In panel c and d, it would be better to show molar concentrations of methane and carbon dioxide in the liquid phase rather than partial pressures in the gas phase, in particular since the conversion is explained in the methods section (L. 149-152). Partial pressures cannot be compared to the molar concentrations of acetate and formate.
Figure 2: The figure is lacking a legend. The title of the x-axis is not capitalized. Check for consistency. “The different symbols indicate three different replicates” – Well, I cannot decipher the information, and I cannot distinguish the different shades of red. The title of the y-axis gives CH₄ and acetate in mM H2. This needs explanation. The figure would benefit from a more concise figure caption.
Figure 3: The figure legend is incomplete. The crosses representing the controls are not present. For methane and carbon dioxide, it would be better to show molar concentrations in the liquid phase rather than partial pressures in the gas phase (see above).
Figure 4: See comments on Figure 2.
Figure 5: The figure is lacking a legend. It is confusing that results for Fuchskuhle are shown in two panels to distinguigh sulfidogenic and methanogenic conditions, while both data sets are combined in one panel for Vercelli. On the y-axis, “per mil vs VPDB” is missing.
Figure 6: The figure legend is unsatisfactory, because it uses abbreviations that are not self-explanatory. The figure caption is not complete, because it is lacking information on the lake sediments. In my opinion, it would be better to present the information in two panels (e.g. (a) without sulfate, (b) with sulfate). Check the spelling of formate.
Figure 7: The figure legend and caption need clarification as suggested for Fig. 1-6. Please add full information on sampling sites, such as rice paddy soil and lake sediment. The abbreviation “IRRI” in introduced in the text, but it would increase readability if the full name was given in the figure caption.
Other minor comments:
L. 111: “The bottles were the amended” seems to contain a typo. Change to “The bottles were amended”
L. 226: “In the rice paddy soils values of δ¹³C increased when formate was being consumed indicating discrimination against the heavy carbon isotope.” This sentence is not clear. Which δ¹³C-values increased? Change to “In the rice paddy soils, δ¹³C-values of formate increased when formate was consumed indicating discrimination against the heavy carbon isotope.”

Citation: https://doi.org/10.5194/egusphere-2023-2279-RC3
- AC2:
  'Reply on RC3', Ralf Conrad, 11 Dec 2023
  
  General comments:
  The formate concentrations in-situ are on the order of micromolar concentrations (Montag & Schink 2018). It is correct that relatively large amounts of formate had to be added to observe a degradation of formate combined with isotope fractionation. In-situ concentrations typically (albeit not always) are steady state concentrations between production and consumption. Under such conditions a compound is consumed after its production without exhibiting kinetic isotope fractionation, simply since everything is consumed without option to preferentially use the light isotope. In order to observe isotope fractionation, it is therefore necessary to increase the concentration of the compound to a level, where the reaction process can exhibit a preference for the light isotope. The criterion for our experiments was the fit of the isotope values of formate to the Mariotti equation, i.e., the of formate versus the logarithm of the fraction of formate utilized. This criterion was fulfilled. We assume that the observation of formate isotope fractionation according to the Wood Ljungdahl pathway would not only be valid that the elevated concentrations where isotope fractionation occurred, but also under steady state conditions, when all the newly produced formate is completely consumed. Perhaps we can add a paragraph with such an explanation to our manuscript.
  As stated in the Experimental Section we incubated the paddy soils at 25°C, but the lake sediments at 10°C, which is the in-situ value.
  
  Specific comments:
  The specific comments all concern proposals to improve the quality of the Figures. We are grateful for the suggestions. It should be no problem to change the figures accordingly.
  
  Citation: https://doi.org/10.5194/egusphere-2023-2279-AC2
  - RC4: 'Reply on AC2', Anonymous Referee #2, 11 Dec 2023
    
    Thank you for the clarification. Yes, I think it would be good to present this explanation in the manuscript as well. My questions have been addressed convincingly, and I don't have additional questions or comments. Yes, my suggestions for the figures should be easy to address, but I hope they will improve readability, and I am looking forward to seeing the final manuscript.
    
    Citation: https://doi.org/10.5194/egusphere-2023-2279-RC4
    
    AC4: 'Reply on RC4', Ralf Conrad, 22 Dec 2023
    
    Thank you for the comments
    
    Citation: https://doi.org/10.5194/egusphere-2023-2279-AC4

Interactive discussion

Status: closed

RC1:
'Comment on egusphere-2023-2279', Anonymous Referee #1, 10 Nov 2023
In this manuscript, the authors report on carbon isotope fractionation during formate transformation in rice paddy soils and lake sediment. They observe formate utilization mainly through homoacetogenesis to be the dominant process that outcompetes methanogenesis and sulfate reduction.
As it appears, the data were collected and evaluated correctly and there is no doubt on their reliability. Nonetheless, it does not become clear why this study was performed and what the outcome is in some few clear sentences. Why was sediment from Fuchskuhle used? Because there were still some 6 years old sediment samples in the coldroom? What are the properties of this specific (and internationally not so well-known) lake (pH, carbonate and sulfate content, trophic status etc.)? Is it representative of freshwater lakes in general? Which general conclusions can be drawn from this study?
Minor comments:
111, l. 120: Omit “the”

190: Sentence unclear.

Fig. 6, correct Formiat to Formate.
307: Energy cannot be generated.

342: equivalents.

403: Where are the data on the 16SrRNA genes?

404: “composition of these genes”? What do the authors mean with that?

425: …are degraded in these paddy soils…

434: author
Citation: https://doi.org/10.5194/egusphere-2023-2279-RC1
- AC1:
  'Reply on RC1', Ralf Conrad, 11 Nov 2023
  
  The incentive for the study is stated in L74-79: “The ε values of methanogenesis or homoacetogenesis from H2 plus CO2 are large (Blaser and Conrad, 2016). However, our knowledge of carbon isotope fractionation with formate as substrate is scarce. In cultures of homoacetogenic bacteria the carbon in the acetate produced from formate was strongly depleted in 13C (ε = -56.5‰) almost similarly as with CO2 as carbon source (Freude and Blaser, 2016). However, it is not known which enrichment factors operate in methanogenic or sulfidogenic environmental samples.” For this purpose, we arbitrarily chose two different methanogenic environments, paddy soil and Lake Fuchskuhle sediments. The reason for chosing them was simply because we had used them before and had background information (e.g. gene sequences). Of course we could have chosen different environments (sewage digestor, peat), but a priori it did not matter in which samples to test for fractionation factors of formate degradation.
  It was during the study of fractionation factors that we realized that formate degradation was dominated by homoacetogenesis, which we found to be intriguing. I must admit that we initially expected that formate would be mainly consumed by methanogenesis. However, this was not the case. We briefly discussed this observation but did not present a theoretical explanation. Perhaps we should speculate about the different molecular mechanisms of formate utilization in acetogens versus methanogens, such as outlined in the recent review by Lemaire et al. (Frontiers Microbiol. 2020). General conclusions are that homoacetogenesis seems to be a major pathway of formate utilization in nature, and that strong fractionation of carbon isotopes occurs mainly during the formation of acetate via the Wood-Ljungdahl pathway, while the initital consumption of formate displayed only a small enrichment factor.
  Lake Fuchskuhle is a lake in Northern Germany, which had been the subject of several studies, also own ones. We can expand the description. For our purpose it was as good as any other lake.
  By the way, the lake sediment was sampled in 2016, and the experiments were performed in 2017. The experiments on paddy soils were done in 2016. We mentioned that the study of formate degradation was one out of three studies that were performed almost in parallel. The other two studies (quoted in the ms) concerned the degradation and isotope fractionation of acetate and of propionate, both previously published in Biogeosciences.
  
  Citation: https://doi.org/10.5194/egusphere-2023-2279-AC1
  - RC2: 'Reply on AC1', Anonymous Referee #1, 13 Nov 2023
    
    The authors have answered my concerns convincingly.
    
    Citation: https://doi.org/10.5194/egusphere-2023-2279-RC2
    
    AC3: 'Reply on RC2', Ralf Conrad, 22 Dec 2023
    
    Thank you for the comments
    
    Citation: https://doi.org/10.5194/egusphere-2023-2279-AC3
RC3:
'Comment on egusphere-2023-2279', Anonymous Referee #2, 04 Dec 2023

General Comments
The manuscript by Conrad and Claus, entitled "Fractionation of stable carbon isotopes during formate consumption in anoxic rice paddy soils and lake sediments" presents an interesting study that analyzes isotope effects associated with formate consumption during incubation experiments. The experiments were conducted with two rice pady soils and two lake sediments, each in triplicate at an incubation temperature of 25°C and over a period of four weeks. The authors have used a straightforward experimental approach and state-of-the art analytical methods, including stable isotope analyses of methane by GC-IRMS and stable isotope analyses of formate and acetate by HPLC-IRMS. They observe formation of acetate from formate with a strong ¹³C-depletion of acetate relative to formate, pointing to homoacetogenesis via the Wood-Ljungdahl pathway.
The scientific questions are relevant and within the scope of BG. The isotopic data are novel. They are discussed in an appropriate and balanced way, and the conclusion is substantial. I couldn't detect major scientific flaws.
My major scientific concern is the amendment of fairly large amounts of formate that produce starting concentrations of more than 15 mM in the incubation experiments. How do these concentrations compare to natural formate levels in paddy soils, lake sediments or other environments? And would formate still be an excellent substrate for acetate production via homoacetogenesis at natural concentration levels? How valid are the findings at 25°C for lake sediments that are generally much colder under in situ conditions? These questions warrant some further discussion.
The manuscript is well organized overall, but the quality of the figures needs improvement. Clear and concise figure captions and legends could improve the readability of the manuscript a lot.
Specific comments and suggestions for the improvement of figures:
Figure 1: The figure legend is incomplete. The crosses representing the controls are not present. Panels c, d and h display a varying shade of red with no clarification. In my opinion, the size of the axis title font is quite small. While the title of the x-axis is capitalized, that of the y-axis is not. In panel e, f, g, and h, it would be appropriate to add "vs VPDB" to the per mil sign on the y-axis. In panel c and d, it would be better to show molar concentrations of methane and carbon dioxide in the liquid phase rather than partial pressures in the gas phase, in particular since the conversion is explained in the methods section (L. 149-152). Partial pressures cannot be compared to the molar concentrations of acetate and formate.
Figure 2: The figure is lacking a legend. The title of the x-axis is not capitalized. Check for consistency. “The different symbols indicate three different replicates” – Well, I cannot decipher the information, and I cannot distinguish the different shades of red. The title of the y-axis gives CH₄ and acetate in mM H2. This needs explanation. The figure would benefit from a more concise figure caption.
Figure 3: The figure legend is incomplete. The crosses representing the controls are not present. For methane and carbon dioxide, it would be better to show molar concentrations in the liquid phase rather than partial pressures in the gas phase (see above).
Figure 4: See comments on Figure 2.
Figure 5: The figure is lacking a legend. It is confusing that results for Fuchskuhle are shown in two panels to distinguigh sulfidogenic and methanogenic conditions, while both data sets are combined in one panel for Vercelli. On the y-axis, “per mil vs VPDB” is missing.
Figure 6: The figure legend is unsatisfactory, because it uses abbreviations that are not self-explanatory. The figure caption is not complete, because it is lacking information on the lake sediments. In my opinion, it would be better to present the information in two panels (e.g. (a) without sulfate, (b) with sulfate). Check the spelling of formate.
Figure 7: The figure legend and caption need clarification as suggested for Fig. 1-6. Please add full information on sampling sites, such as rice paddy soil and lake sediment. The abbreviation “IRRI” in introduced in the text, but it would increase readability if the full name was given in the figure caption.
Other minor comments:
L. 111: “The bottles were the amended” seems to contain a typo. Change to “The bottles were amended”
L. 226: “In the rice paddy soils values of δ¹³C increased when formate was being consumed indicating discrimination against the heavy carbon isotope.” This sentence is not clear. Which δ¹³C-values increased? Change to “In the rice paddy soils, δ¹³C-values of formate increased when formate was consumed indicating discrimination against the heavy carbon isotope.”

Citation: https://doi.org/10.5194/egusphere-2023-2279-RC3
- AC2:
  'Reply on RC3', Ralf Conrad, 11 Dec 2023
  
  General comments:
  The formate concentrations in-situ are on the order of micromolar concentrations (Montag & Schink 2018). It is correct that relatively large amounts of formate had to be added to observe a degradation of formate combined with isotope fractionation. In-situ concentrations typically (albeit not always) are steady state concentrations between production and consumption. Under such conditions a compound is consumed after its production without exhibiting kinetic isotope fractionation, simply since everything is consumed without option to preferentially use the light isotope. In order to observe isotope fractionation, it is therefore necessary to increase the concentration of the compound to a level, where the reaction process can exhibit a preference for the light isotope. The criterion for our experiments was the fit of the isotope values of formate to the Mariotti equation, i.e., the of formate versus the logarithm of the fraction of formate utilized. This criterion was fulfilled. We assume that the observation of formate isotope fractionation according to the Wood Ljungdahl pathway would not only be valid that the elevated concentrations where isotope fractionation occurred, but also under steady state conditions, when all the newly produced formate is completely consumed. Perhaps we can add a paragraph with such an explanation to our manuscript.
  As stated in the Experimental Section we incubated the paddy soils at 25°C, but the lake sediments at 10°C, which is the in-situ value.
  
  Specific comments:
  The specific comments all concern proposals to improve the quality of the Figures. We are grateful for the suggestions. It should be no problem to change the figures accordingly.
  
  Citation: https://doi.org/10.5194/egusphere-2023-2279-AC2
  - RC4: 'Reply on AC2', Anonymous Referee #2, 11 Dec 2023
    
    Thank you for the clarification. Yes, I think it would be good to present this explanation in the manuscript as well. My questions have been addressed convincingly, and I don't have additional questions or comments. Yes, my suggestions for the figures should be easy to address, but I hope they will improve readability, and I am looking forward to seeing the final manuscript.
    
    Citation: https://doi.org/10.5194/egusphere-2023-2279-RC4
    
    AC4: 'Reply on RC4', Ralf Conrad, 22 Dec 2023
    
    Thank you for the comments
    
    Citation: https://doi.org/10.5194/egusphere-2023-2279-AC4

Peer review completion

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

ED: Publish subject to minor revisions (review by editor) (01 Jan 2024) by Perran Cook

AR by Ralf Conrad on behalf of the Authors (03 Jan 2024) Author's response Author's tracked changes Manuscript

ED: Publish as is (08 Feb 2024) by Perran Cook

AR by Ralf Conrad on behalf of the Authors (12 Feb 2024) Author's response Manuscript

Journal article(s) based on this preprint

11 Mar 2024

Fractionation of stable carbon isotopes during formate consumption in anoxic rice paddy soils and lake sediments

Ralf Conrad and Peter Claus

Biogeosciences, 21, 1161–1172, https://doi.org/10.5194/bg-21-1161-2024,https://doi.org/10.5194/bg-21-1161-2024, 2024

Short summary

Ralf Conrad and Peter Claus

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Ralf Conrad and Peter Claus

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Knowledge of carbon isotope fractionation is important for the assessment of the pathways involved in the degradation of organic matter. Formate is an important intermediate during this process. It was mainly converted to carbon dioxide and acetate both in the presence and absence of sulfate. Methane was only a minor product and was mainly formed from the acetate. The acetate was depleted in the heavy carbon atom relative to formate, while the carbon dioxide was enriched.


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