the Creative Commons Attribution 4.0 License.
the Creative Commons Attribution 4.0 License.
| 25 Jun 2024
Exometabolomic exploration of culturable airborne microorganisms from an urban atmosphere
Abstract. The interactions of metabolically active atmospheric microorganisms with cloud organic matter can alter the atmospheric carbon cycle. Upon deposition, atmospheric microorganisms can influence microbial communities in surface Earth systems. However, the metabolic activities of cultivable atmospheric microorganisms in settled habitats remain less understood. Here, we investigated exometabolites produced by typical bacterial and fungal species isolated from the urban atmosphere to elucidate their biogeochemical roles. Molecular compositions of exometabolites were analyzed using ultra-high resolution Fourier transform ion cyclotron resonance mass spectrometry. Annotation through the Kyoto Encyclopedia of Genes and Genomes database helped identify metabolic processes. Results showed that bacterial and fungal strains produce exometabolites with lower H/C and higher O/C ratios than consumed and resistant compounds. CHON compounds constituted over 50 % of the identified formulas of exometabolites. Bacterial exometabolites contained more abundant CHONS compounds (25.2 %), while fungal exometabolites were rich in CHO compounds (31.7 %). These microbial exometabolites predominantly comprised aliphatic/peptide-like and carboxyl-rich alicyclic molecules (CRAM-like). Significant variations in metabolites were observed among different strains. Bacteria showed a performance for amino acid synthesis, while fungi were more active in transcription and expression processes. Lipid metabolism, amino acid metabolism, and carbohydrate metabolism varied widely among bacterial strains, while fungi exhibited marked differences in carbohydrate metabolism and secondary metabolism. This comprehensive examination of metabolite characteristics at the molecular level for typical culturable airborne microorganisms enhances our understanding of their potential metabolic activities at air-land/water interfaces. These insights are pivotal for assessing the biogeochemical impacts of atmospheric microorganisms following their deposition.
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RC1: 'Comment on egusphere-2024-1880', Anonymous Referee #1, 01 Jul 2024
This work from Jin et al., titled with “Exometabolomic exploration of culturable airborne microorganisms from an urban atmosphere” has investigated the metabolic activity of airborne culturable microorganisms at the molecule level. Distinct metabolic profiles were observed for the different bacterial strains and the fungal strains. Some suggestions are as below:
It is interesting to reveal the different metabolic profile of microorganisms isolated from the ambient air. How about the abundance of these unique “produced” products in the ambient air?
The introduction is somewhat lengthy; it is recommended to condense and refine it appropriately.
Lines 150-160: why the culture process were repeated for three cycles? What is the rationale behind this? Bacteria were culture at 37 oC and fungi were cultured at 28 oC. Why these two temperatures were selected? will the culture temperature affect the exometabolome?
Lines 223: what does this word “resistant” mean here?
Figure 2 panel b: it would be better to label each column. Otherwise, it is not clear which bar is the consumed, resistant, and produced organic matter.
Figure 4 pane a: I assume that the two pie charts represent the distribution of number concentration and intensity concentration, respectively. if yes, it might be better to use different color scales for these two charts to differentiate them. Similar suggestion for figure 5a.
Citation: https://doi.org/10.5194/egusphere-2024-1880-RC1 -
RC2: 'Comment on egusphere-2024-1880', Teruya Maki, 03 Aug 2024
General comments
This paper reported on the exometabolite (extracellular chemical components) produced by microbial cultures, which are isolated from urban aerosol samples. Investigating the extracellular components from airborne microorganisms are important for understanding the nutrient input by deposition, the survival of airborne microorganisms, the microbial growth, the chemical cycles, the pathogenic strategy and so on. However, I think this paper just showed the measurement data of exometabolite discussing no categorization of ecological means for each isolates producing exometabolite. Additionally, although there are several species of isolates, the exometabolite producing by each species are not categorized and the ecological characteristics of exometabolite have not discussed clearly.
I think this manuscript could be accepted after redrafting the manuscript.
Some major comments:
- I think the total twelve strains are small for discussing the contribution of organic materials to carborne cycles in atmosphere, because there are many kinds of airborne microorganisms, which are unculturable (>90% of microorganisms cannot be cultured but they are living). The authors should discuss deeply on microbial compositions to focus on the dominant species, which can be focused as keystone species.
- Extracellular products are composed of several kinds of chemical components, which contribute to the roles of airborne microorganisms. Accordingly, after the categories of ecological merits by the chemical components are defined, the categories of chemical components are established for understanding the roles of extracellular products on airborne bacterial ecology. For examples, there are the some categories such as 1) Survivals of airborne microorganisms in atmosphere, 2) Microbial growth in atmosphere and after deposition, 3) Chemical cycles in several environments, and 4) Pathogenic abilities using some components and so on.
- The six isolates of bacteria or fungi can be classified to some groups in dependence on the taxon. The chemical components in extracellular products are discussed for each category to understand the ecological characteristics of each categorized microorganisms. This comments are relating to Comment 1.
- The Results and Discussion should be separated each, because there are many overlapped parts and redundancy, which make readers understand this hardly.
- I think the authors are not familiar with biology. So some biologist suggestion is needed for categorizing the taxon and describing the taxon manes.
Some minor comments:
L19: What is CHON?
L22: Fungi also produce amino acid.
L25-L28: This is general summary. Please summarize specific topics for this study.
L30-L40: The sampling is performed in Asian site. The papers relating to Asian-dust transport of bioaerosols are needed. I think European bioaerosols are different from Asian bioaerosols. So the author can isolate the Bacillus strain efficiently.
L64-L65: This is not related to the organic matters.
L83-L90: This sampling site is located in Asia. How is Asian dust events?
L91-L101: The analytical methos should be the results relating to more ecological topics. I think this section just show analytical method index.
L110: I do not think KEGG analysis is needed for this paper. However, if KEGG analysis is remained, the KEGG analysis should be introduce in the introduction section.
L123: How many samples are collected? The sample numbers should be describe and the samples for each isolates are explained. Additionally, the environmental factors have to be discussed when the isolates are obtained.
L184-L185: The chemical components should be defined in detail, because these are familiar with the readers for ACP.
L185: KEGG explanation is needed in the Introduction. Why was this used for this paper?
L193: As described, I recommend to separate to each section of Result and Discussion.
L196-L197: The strain numbers should be described.
L262: The genus name should be initial after second using. For example, A. niger. This is biological rule.
Fig.1. The new phyla name of bacteria should be used.
L362-L430: This section is overlapped to Section 3.2. Please combine them.
Citation: https://doi.org/10.5194/egusphere-2024-1880-RC2 -
RC3: 'Comment on egusphere-2024-1880', Anonymous Referee #3, 06 Aug 2024
In this study, the authors examined the microbial exometabolism production of culturable airborne microorganisms from an urban atmosphere. A diverse range of products, including CHON, CHONS, and CHO compounds, were identified for both bacteria and fungi. Significant variations in metabolites were observed among different strains. In terms of amino acid synthesis, transcription and expression processes, lipid metabolism, amino acid metabolism, and carbohydrate metabolism, there was a wide variation among bacterial and fungal species. The results provide a comprehensive examination of metabolite characteristics at the molecular level for typical culturable airborne microorganisms. Overall, this work is novel and interesting, and the ideas and data presented in the manuscript are credible. This paper could be accepted after appropriately revision. More detailed comments/suggestions are provided below.
- L78 The influence of dry deposition dust on marine terrestrial ecological environments was discussed, with a particular focus on microbial communities. Additionally, the effects of wet deposition, including cloud, fog, rain, or snow processes should clarify.
- Line 102-109, this section is an introduction to the FT-ICR MS method, which could be integrated into section 2. Materials and methods.
- Line 123, the sampling period is three days, yet it remains unclear whether the sample volum satisfies the prerequisites for analysis. Could you elucidate the criteria employed to determine the sampling dates? Were these days being clean, polluted, or sunny or rainy/snowy days? Furthermore, could you elaborate on why the sampling time was specifically set between 15:00-19:00? Please offer further insights into the sampling procedure.
- Line 132, the methodology for microbial culture and separation must be detailed, including specific parameters such as centrifugal speed and the volume of bacteria collected.
- Line 158-160, the culture time of bacteria is 7 days, and fungi is 15 days. Is there any reference for the culture time? Or refer to the residence time of microorganisms in the atmosphere? In Line 241, whether the results of different times are comparable compared to the results of culture for 30 days?
- Line 198, here discussed the genus of Pantoea, is Pantoea also a dominant bacterium? Another predominant strain, Streptomyces, was not further explained.
- Line 279, the diversity of exometabolomic products in bacteria and fungi is not analogous, hence a comparison between the two is not advisable. However, it is permissible to separately compare bacterial diversity across different samples and fungal diversity across different samples.
- Line325, it is advised to omit the comparison between bacteria and fungi.
- section 3.4 “Metabolic processes of typical isolated bacterial and fungal strains”, the discussion of metabolic processes in bacterial and fungal in 3.4.1 and 3.4.2 is separate. In fact, in the atmosphere, the metabolism of bacteria and fungi is closely related. The authors can add a discussion of correlations between bacterial and fungal metabolic processes, thus the influence of the metabolic process of bacteria and fungi on atmospheric environment and biogeochemical cycles can be further clarified.
Citation: https://doi.org/10.5194/egusphere-2024-1880-RC3 -
AC1: 'Response to comments from reviewers-egusphere-2024-1880', Wei HU, 28 Sep 2024
The comment was uploaded in the form of a supplement: https://egusphere.copernicus.org/preprints/2024/egusphere-2024-1880/egusphere-2024-1880-AC1-supplement.pdf
Status: closed
-
RC1: 'Comment on egusphere-2024-1880', Anonymous Referee #1, 01 Jul 2024
This work from Jin et al., titled with “Exometabolomic exploration of culturable airborne microorganisms from an urban atmosphere” has investigated the metabolic activity of airborne culturable microorganisms at the molecule level. Distinct metabolic profiles were observed for the different bacterial strains and the fungal strains. Some suggestions are as below:
It is interesting to reveal the different metabolic profile of microorganisms isolated from the ambient air. How about the abundance of these unique “produced” products in the ambient air?
The introduction is somewhat lengthy; it is recommended to condense and refine it appropriately.
Lines 150-160: why the culture process were repeated for three cycles? What is the rationale behind this? Bacteria were culture at 37 oC and fungi were cultured at 28 oC. Why these two temperatures were selected? will the culture temperature affect the exometabolome?
Lines 223: what does this word “resistant” mean here?
Figure 2 panel b: it would be better to label each column. Otherwise, it is not clear which bar is the consumed, resistant, and produced organic matter.
Figure 4 pane a: I assume that the two pie charts represent the distribution of number concentration and intensity concentration, respectively. if yes, it might be better to use different color scales for these two charts to differentiate them. Similar suggestion for figure 5a.
Citation: https://doi.org/10.5194/egusphere-2024-1880-RC1 -
RC2: 'Comment on egusphere-2024-1880', Teruya Maki, 03 Aug 2024
General comments
This paper reported on the exometabolite (extracellular chemical components) produced by microbial cultures, which are isolated from urban aerosol samples. Investigating the extracellular components from airborne microorganisms are important for understanding the nutrient input by deposition, the survival of airborne microorganisms, the microbial growth, the chemical cycles, the pathogenic strategy and so on. However, I think this paper just showed the measurement data of exometabolite discussing no categorization of ecological means for each isolates producing exometabolite. Additionally, although there are several species of isolates, the exometabolite producing by each species are not categorized and the ecological characteristics of exometabolite have not discussed clearly.
I think this manuscript could be accepted after redrafting the manuscript.
Some major comments:
- I think the total twelve strains are small for discussing the contribution of organic materials to carborne cycles in atmosphere, because there are many kinds of airborne microorganisms, which are unculturable (>90% of microorganisms cannot be cultured but they are living). The authors should discuss deeply on microbial compositions to focus on the dominant species, which can be focused as keystone species.
- Extracellular products are composed of several kinds of chemical components, which contribute to the roles of airborne microorganisms. Accordingly, after the categories of ecological merits by the chemical components are defined, the categories of chemical components are established for understanding the roles of extracellular products on airborne bacterial ecology. For examples, there are the some categories such as 1) Survivals of airborne microorganisms in atmosphere, 2) Microbial growth in atmosphere and after deposition, 3) Chemical cycles in several environments, and 4) Pathogenic abilities using some components and so on.
- The six isolates of bacteria or fungi can be classified to some groups in dependence on the taxon. The chemical components in extracellular products are discussed for each category to understand the ecological characteristics of each categorized microorganisms. This comments are relating to Comment 1.
- The Results and Discussion should be separated each, because there are many overlapped parts and redundancy, which make readers understand this hardly.
- I think the authors are not familiar with biology. So some biologist suggestion is needed for categorizing the taxon and describing the taxon manes.
Some minor comments:
L19: What is CHON?
L22: Fungi also produce amino acid.
L25-L28: This is general summary. Please summarize specific topics for this study.
L30-L40: The sampling is performed in Asian site. The papers relating to Asian-dust transport of bioaerosols are needed. I think European bioaerosols are different from Asian bioaerosols. So the author can isolate the Bacillus strain efficiently.
L64-L65: This is not related to the organic matters.
L83-L90: This sampling site is located in Asia. How is Asian dust events?
L91-L101: The analytical methos should be the results relating to more ecological topics. I think this section just show analytical method index.
L110: I do not think KEGG analysis is needed for this paper. However, if KEGG analysis is remained, the KEGG analysis should be introduce in the introduction section.
L123: How many samples are collected? The sample numbers should be describe and the samples for each isolates are explained. Additionally, the environmental factors have to be discussed when the isolates are obtained.
L184-L185: The chemical components should be defined in detail, because these are familiar with the readers for ACP.
L185: KEGG explanation is needed in the Introduction. Why was this used for this paper?
L193: As described, I recommend to separate to each section of Result and Discussion.
L196-L197: The strain numbers should be described.
L262: The genus name should be initial after second using. For example, A. niger. This is biological rule.
Fig.1. The new phyla name of bacteria should be used.
L362-L430: This section is overlapped to Section 3.2. Please combine them.
Citation: https://doi.org/10.5194/egusphere-2024-1880-RC2 -
RC3: 'Comment on egusphere-2024-1880', Anonymous Referee #3, 06 Aug 2024
In this study, the authors examined the microbial exometabolism production of culturable airborne microorganisms from an urban atmosphere. A diverse range of products, including CHON, CHONS, and CHO compounds, were identified for both bacteria and fungi. Significant variations in metabolites were observed among different strains. In terms of amino acid synthesis, transcription and expression processes, lipid metabolism, amino acid metabolism, and carbohydrate metabolism, there was a wide variation among bacterial and fungal species. The results provide a comprehensive examination of metabolite characteristics at the molecular level for typical culturable airborne microorganisms. Overall, this work is novel and interesting, and the ideas and data presented in the manuscript are credible. This paper could be accepted after appropriately revision. More detailed comments/suggestions are provided below.
- L78 The influence of dry deposition dust on marine terrestrial ecological environments was discussed, with a particular focus on microbial communities. Additionally, the effects of wet deposition, including cloud, fog, rain, or snow processes should clarify.
- Line 102-109, this section is an introduction to the FT-ICR MS method, which could be integrated into section 2. Materials and methods.
- Line 123, the sampling period is three days, yet it remains unclear whether the sample volum satisfies the prerequisites for analysis. Could you elucidate the criteria employed to determine the sampling dates? Were these days being clean, polluted, or sunny or rainy/snowy days? Furthermore, could you elaborate on why the sampling time was specifically set between 15:00-19:00? Please offer further insights into the sampling procedure.
- Line 132, the methodology for microbial culture and separation must be detailed, including specific parameters such as centrifugal speed and the volume of bacteria collected.
- Line 158-160, the culture time of bacteria is 7 days, and fungi is 15 days. Is there any reference for the culture time? Or refer to the residence time of microorganisms in the atmosphere? In Line 241, whether the results of different times are comparable compared to the results of culture for 30 days?
- Line 198, here discussed the genus of Pantoea, is Pantoea also a dominant bacterium? Another predominant strain, Streptomyces, was not further explained.
- Line 279, the diversity of exometabolomic products in bacteria and fungi is not analogous, hence a comparison between the two is not advisable. However, it is permissible to separately compare bacterial diversity across different samples and fungal diversity across different samples.
- Line325, it is advised to omit the comparison between bacteria and fungi.
- section 3.4 “Metabolic processes of typical isolated bacterial and fungal strains”, the discussion of metabolic processes in bacterial and fungal in 3.4.1 and 3.4.2 is separate. In fact, in the atmosphere, the metabolism of bacteria and fungi is closely related. The authors can add a discussion of correlations between bacterial and fungal metabolic processes, thus the influence of the metabolic process of bacteria and fungi on atmospheric environment and biogeochemical cycles can be further clarified.
Citation: https://doi.org/10.5194/egusphere-2024-1880-RC3 -
AC1: 'Response to comments from reviewers-egusphere-2024-1880', Wei HU, 28 Sep 2024
The comment was uploaded in the form of a supplement: https://egusphere.copernicus.org/preprints/2024/egusphere-2024-1880/egusphere-2024-1880-AC1-supplement.pdf
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