the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
| 09 Nov 2023
Bacteria in clouds biodegrade atmospheric formic and acetic acids
Abstract. Formic and acetic acids are major organic species in cloud water and affect precipitation acidity. In current atmospheric models, their losses are limited to chemical oxidation in the gas and aqueous phases and deposition processes. Previous lab studies suggest that these acids can be efficiently biodegraded in water by atmospherically relevant bacteria. However, the importance of biodegradation as a loss process in the atmospheric multiphase system has not been fully assessed. We implemented biodegradation as an additional sink of formic and acetic acids in a detailed atmospheric multiphase chemistry model. In our model, biodegradation is considered in a small subset of cloud droplets according to atmospheric bacteria concentrations of 0.1 cm−3. We predict that up to 20 ppt h−1 formic acid and 5 ppt h−1 acetic acid are biodegraded, affecting the total change of acid concentrations by 20 % and 3 %, respectively. Our model sensitivity studies suggest that acetic acid is most efficiently biodegraded at high cloud water pH (> 5) whereas biodegradation is least efficient for formic acid under such conditions. This trend is explained by the higher solubility of formic acid (high effective Henry’s law constant) that results in less evaporation from bacteria-free and subsequent uptake into bacteria-containing droplets. Our analysis demonstrates that previous estimates of the importance of atmospheric biodegradation were often biased high as they did not correctly account for such diffusion limitation of phase transfer processes between droplets. The results suggest that under specific conditions, biological processes can significantly affect atmospheric composition and concentrations in particular of volatile, moderately soluble organics.
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RC1: 'Comment on egusphere-2023-2270', Anonymous Referee #1, 11 Dec 2023
Review of Bacteria in clouds biodegrade atmospheric formic and acetic acids
By Lopez et al.
This work describes implementation of biodegradation loss rates for formic and acetic acids as in a detailed model of atmospheric gas and aqueous phase chemistry. There are few groups who can reliably do both chemical and biological modeling of clouds with skill. The novelty of this work, is that through explicit accounting of kinetic mass transfer limits during phase transfer processes between droplets, the authors find that biodegradation rates outpace chemical rates, which in contrary to conventional wisdom. The authors predict up to 20 ppt h^−1 formic acid and 5 ppt h^−1 acetic acid are biodegraded. The description of abiotic chemistry is much more complex than the microbiology. I think the authors seek to understand to what degree microbiology can compete with chemistry and are working to understand limits and boundaries. I am not an expert on microbiology.
I think this is important work suitable for publication provided the following comments and questions can be addressed.
My main concerns relate to how well the description of microbial biodegradation rates accurately reflect atmospheric processes. There is discussion on how abiotic chemical oxidation changes with temperature and pH, but not for biotic biodegradation. On Line 74, the kbact rate employed for biodegradation is taken to be empirical for 17C (290K), while the simulations are at 286K. Do biodegradation rates change over this temperature range? Also, how representative is the chosen temperature representative of cloud conditions? If a temperature sensitivity was performed, would biodegradation rates be sufficiently well characterized so that we accurately understand the temperature dependence of the abiotic vs. biotic competition? How about for pH? It is difficult to understand how accurate the findings regarding pH dependence are, given the neglect of pH consideration for the biodegradation rates.
I understand how Equation 7 is derived given constant values of LWC and bacteria. I am comfortable with the idea that an air parcel has a given amount of LWC that is distributed over the available activation particles. Is a similar approach for bacteria reasonable? Can the authors back up this assumption for bacteria?
Specific comments:
Line 10: instead of (high effective Henry’s law coefficient) , which is subjective - it would be better to list both the FA and AA Heff values.
Line 11: “…from bacteria-free and subsequent uptake into bacteria-containing droplets ….” This is awkwardly written and hard to understand.
Line 50: The authors state “Species concentrations in the atmosphere are much lower than in the denser soil; however, the atmospheric volume is much larger as compared to the biotic terrestrial and aquatic environments. Therefore, it seems reasonable to infer a potential role of biodegradation as a competitive sink to other atmospheric loss processes”. Is that right? It is not the volume of atmospheric water, not the total atmosphere, that is available for biodegradation?
The Figure 2 caption should include an explanation of the isopleths.
Does Fig 3 present the initial aqueous phase concentrations or are calculations for a give cloud processing time presented?
Editorial
Line 21: grammar “…are ubiquitous main components of the global …” Ubiquitous main reads a little awkwardly and should be rephrased.
Line 50: “… as a competitive sink to other atmospheric…” This reads a little awkwardly. I think the authors mean to say “competitive sink relative to ..." However, as described above, I am not sure they make this point
Line 92: I think “a” is missing between “to” and “second”
Line 99: I think “were” should be ‘is’ The paper is written in the present tense and biodegradation is singular.
Fig. 3 caption, should delta D be delta C?
Citation: https://doi.org/10.5194/egusphere-2023-2270-RC1 -
RC2: 'Comment on egusphere-2023-2270', Anonymous Referee #2, 06 Feb 2024
The authors present a modeling study of the impact of bacterial metabolism of acetic and formic acids in cloud water and its impact on the atmospheric chemistry of these species. The topic is important, since the chemistry of formic acid in the upper atmosphere is not well understood and it has been suspected for some time that cloud chemistry and possibly biology play critical roles. The premise of this study is similar to that of Fankhauser et al. (2019) who did a similar simulation in the GAMMA model, considering more organic species in both cloud droplets and aqueous aerosols in equilibrium with the gas phase. Although the fundamental chemistry and physics (and biology) in the models is similar, the authors emphasize that the important difference (other than the simulated droplet life cycle) is that the current study simulates an ensemble of droplets rather than focusing on a single droplet in equilibrium with the gas phase. The authors posit that droplet-gas-droplet partitioning between droplets in the ensemble towards the droplets containing bacteria enhances the impact of bacteria on the organic acid budget despite the low total number of droplets containing bacteria in the ensemble. This is logical but most likely overstated in this study. The droplets in Fankhauser et al. were in equilibrium with the gas phase, and formic acid levels in the gas phase were not depleted by microbial activity on the timescale of the simulation (see, e.g. Figure S3 of that paper)- that is, the destruction of formic acid in the droplets was not limited by partitioning from the gas phase and any hypothetical partitioning to the gas phase from other cloud droplets would not have impacted this. The authors need to add some more nuance to their discussion of Fankhauser et al.
Citation: https://doi.org/10.5194/egusphere-2023-2270-RC2 -
AC1: 'Author response to both referee comments', Leslie Nuñez López, 07 Mar 2024
The comment was uploaded in the form of a supplement: https://egusphere.copernicus.org/preprints/2023/egusphere-2023-2270/egusphere-2023-2270-AC1-supplement.pdf
Status: closed
-
RC1: 'Comment on egusphere-2023-2270', Anonymous Referee #1, 11 Dec 2023
Review of Bacteria in clouds biodegrade atmospheric formic and acetic acids
By Lopez et al.
This work describes implementation of biodegradation loss rates for formic and acetic acids as in a detailed model of atmospheric gas and aqueous phase chemistry. There are few groups who can reliably do both chemical and biological modeling of clouds with skill. The novelty of this work, is that through explicit accounting of kinetic mass transfer limits during phase transfer processes between droplets, the authors find that biodegradation rates outpace chemical rates, which in contrary to conventional wisdom. The authors predict up to 20 ppt h^−1 formic acid and 5 ppt h^−1 acetic acid are biodegraded. The description of abiotic chemistry is much more complex than the microbiology. I think the authors seek to understand to what degree microbiology can compete with chemistry and are working to understand limits and boundaries. I am not an expert on microbiology.
I think this is important work suitable for publication provided the following comments and questions can be addressed.
My main concerns relate to how well the description of microbial biodegradation rates accurately reflect atmospheric processes. There is discussion on how abiotic chemical oxidation changes with temperature and pH, but not for biotic biodegradation. On Line 74, the kbact rate employed for biodegradation is taken to be empirical for 17C (290K), while the simulations are at 286K. Do biodegradation rates change over this temperature range? Also, how representative is the chosen temperature representative of cloud conditions? If a temperature sensitivity was performed, would biodegradation rates be sufficiently well characterized so that we accurately understand the temperature dependence of the abiotic vs. biotic competition? How about for pH? It is difficult to understand how accurate the findings regarding pH dependence are, given the neglect of pH consideration for the biodegradation rates.
I understand how Equation 7 is derived given constant values of LWC and bacteria. I am comfortable with the idea that an air parcel has a given amount of LWC that is distributed over the available activation particles. Is a similar approach for bacteria reasonable? Can the authors back up this assumption for bacteria?
Specific comments:
Line 10: instead of (high effective Henry’s law coefficient) , which is subjective - it would be better to list both the FA and AA Heff values.
Line 11: “…from bacteria-free and subsequent uptake into bacteria-containing droplets ….” This is awkwardly written and hard to understand.
Line 50: The authors state “Species concentrations in the atmosphere are much lower than in the denser soil; however, the atmospheric volume is much larger as compared to the biotic terrestrial and aquatic environments. Therefore, it seems reasonable to infer a potential role of biodegradation as a competitive sink to other atmospheric loss processes”. Is that right? It is not the volume of atmospheric water, not the total atmosphere, that is available for biodegradation?
The Figure 2 caption should include an explanation of the isopleths.
Does Fig 3 present the initial aqueous phase concentrations or are calculations for a give cloud processing time presented?
Editorial
Line 21: grammar “…are ubiquitous main components of the global …” Ubiquitous main reads a little awkwardly and should be rephrased.
Line 50: “… as a competitive sink to other atmospheric…” This reads a little awkwardly. I think the authors mean to say “competitive sink relative to ..." However, as described above, I am not sure they make this point
Line 92: I think “a” is missing between “to” and “second”
Line 99: I think “were” should be ‘is’ The paper is written in the present tense and biodegradation is singular.
Fig. 3 caption, should delta D be delta C?
Citation: https://doi.org/10.5194/egusphere-2023-2270-RC1 -
RC2: 'Comment on egusphere-2023-2270', Anonymous Referee #2, 06 Feb 2024
The authors present a modeling study of the impact of bacterial metabolism of acetic and formic acids in cloud water and its impact on the atmospheric chemistry of these species. The topic is important, since the chemistry of formic acid in the upper atmosphere is not well understood and it has been suspected for some time that cloud chemistry and possibly biology play critical roles. The premise of this study is similar to that of Fankhauser et al. (2019) who did a similar simulation in the GAMMA model, considering more organic species in both cloud droplets and aqueous aerosols in equilibrium with the gas phase. Although the fundamental chemistry and physics (and biology) in the models is similar, the authors emphasize that the important difference (other than the simulated droplet life cycle) is that the current study simulates an ensemble of droplets rather than focusing on a single droplet in equilibrium with the gas phase. The authors posit that droplet-gas-droplet partitioning between droplets in the ensemble towards the droplets containing bacteria enhances the impact of bacteria on the organic acid budget despite the low total number of droplets containing bacteria in the ensemble. This is logical but most likely overstated in this study. The droplets in Fankhauser et al. were in equilibrium with the gas phase, and formic acid levels in the gas phase were not depleted by microbial activity on the timescale of the simulation (see, e.g. Figure S3 of that paper)- that is, the destruction of formic acid in the droplets was not limited by partitioning from the gas phase and any hypothetical partitioning to the gas phase from other cloud droplets would not have impacted this. The authors need to add some more nuance to their discussion of Fankhauser et al.
Citation: https://doi.org/10.5194/egusphere-2023-2270-RC2 -
AC1: 'Author response to both referee comments', Leslie Nuñez López, 07 Mar 2024
The comment was uploaded in the form of a supplement: https://egusphere.copernicus.org/preprints/2023/egusphere-2023-2270/egusphere-2023-2270-AC1-supplement.pdf
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