Study on Genomics of the Bisphenol A-Degrading Bacterium Pseudomonas sp. P1

Round 1

Reviewer 1 Report

The manuscript studied the Genomics of a Bisphenol A (BPA)-degrading strain Pseudomonas sp. P1. A series of tests were performed to characterize the biodegradation of BPA and its mechanism. It provides new documentation of a bacteria with high efficiency and adaptation ability for the degradation BPA in water. However, there are several syntax and grammar errors in the text. Some details in the experiment are not provided. Results and discussion are somewhat tedious. Specific comments are shown below.

1.     In abstract, Line 19, “degradation” should be “degradation.”. In Line 26, “P1” should be “strain P1”. Lines 25-26, the sentence “it was explained that P1 had good tolerance to various environmental factors and enriched the degradation mechanism of BPA” is confusing. Who “enriched the degradation……”? Line 75, “degrading” should be “degrade”.

2.     In introduction, Lines 41-42, what are the concentration of BPA in natural water environment such as surface water and groundwater? The data should be provided.

3.     In Lines 90-101, what is the purpose or objective of the study? It should be clearly stated.

4.     In Line 103, “drug” may be changed to “chemicals”.

5.     In Line 116, what is the composition of MSM? It should be provided.

6.     In Lines 140-141, how to keep the sterile condition “aseptic”?

7.     In Lines 131-145, what containers were used for the test? How much was the volume of the medium? How much was taken periodically for the measurement of biomass and BPA concentration?

8.     In Lines 146-149, how the BPA degradation metabolites were detected?

9.     In Line 150, Table 1 is confusing. “Gradient level” is not “Factors”. The set up of the conditions is not clear.

10.   In Line 167, “))” should be “)”.

11.   In Line 173, “by PCR were detected” may be changed to “were detected by PCR”.

12.   In Lines 172-184, how DNA or RNA were extracted？

13.   In line 189, how “aerobic” condition was obtained?

14.   In line 214, “We obtained the functional annotation of the gene……” may be changed to “The functional annotation of the gene was obtained……”.

15.   In Line 220, “aromatic compounds” may be removed, since xylene and polycyclic aromatic hydrocarbons are also aromatic compounds.

16.   In Lines 324-325, “the degradation rate of strain P1 was more than 50%” is too general. The specific data should be provided and better put in Line 323.

17.   In Line 326, “bpa” should be “BPA”.

18.   In Line 327, “in the concentration range of 30 mg/L”, there is no range.

19.   In Figure 3 B, Line 349, the words for the first two legends are not appropriate.

20.     In Lines 354-405, since SOD, CAT and GSH were not measured in this study, this section may be shortened.  

Author Response

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Author Response File: Author Response.docx

Reviewer 2 Report

Manuscript No.  water-2189977

Title: Study on Genomics of the Bisphenol A degrading bacterium 2 Pseudomonas sp. P1

The authors studied and reported on Genomics of the Bisphenol A degrading bacterium 2 Pseudomonas sp. P1. The manuscript was well organized and the was properly discussed. The work was suitable for the publication. However, it need to improve, few key points need to be addressed.

1.      Abstract has to write precisely.

2.      Introduction needs to be discussed more.

https://www.sciencedirect.com/science/article/abs/pii/S0048969722076744?via%3Dihub

https://www.sciencedirect.com/science/article/abs/pii/S014765131630433X

https://link.springer.com/referenceworkentry/10.1007/978-3-319-58538-3_230-1

3.      Discussion part has to be improved

4.       Conclusion part has to be improved

5.      Grammatical errors and Spelling mistakes needs to be corrected.

Author Response

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Author Response File: Author Response.docx

Reviewer 3 Report

 The manuscript presents very interesting studies, the manuscript is well structured and written, and the experiment is well designed. However, it would be advisable to improve the paper before accepting:

1.       Line 104-105 – please provide the geographical coordinates of the sample collection site.

2.    Line 116 – please provide the detailed composition of the inorganic MSM medium. In this section, there is also no information about the bacteria isolation (or extraction from the Environmental matrix) step. Please provide it.

3.       Line 118 – how the BPA was detected? Please specify.

4.       It is unclear to me the origin of the P1 strain. Did your science group isolate it? If yes, why did you choose this strain, was it the most effective?

5.       Line 131-138 – I suggest transferring this to the introduction section. This is not a description of BPA degradation method.

6.       2.4 section – genome sequencing. Please provide information about the methods of DNA isolation and DNA quantitation.

7.       In lines 194-197 Authors describe the cell analysis (microscopic and functional). There was no information about this method in the materials and methods section. Please provide it.

8.       The Figure 5 is unreadable. Is it possible to increase the font?

Author Response

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Reviewer 4 Report

The search for effective methods of neutralization and biodegradation of bisphenol A (BPA) remains an urgent and modern problem. Indeed, the genetic aspects of BPA biodegradation are not well understood; in this regard, this manuscript is of interest to the reader.

General comments: 

- Authors did not mention other works reporting Pseudomonas spp. as BPA biodegraders but there are many of them (https://doi.org/10.1186/s12866-020-1699-9, https://doi.org/10.1016/j.jrras.2017.08.003, https://link.springer.com/article/10.1007 /s10532-022-10003-4, https://doi.org/10.1007/s00203-022-02885-y, https://doi.org/10.1080/00986445.2021.2012462, https://doi.org/10.1039 /D2RA06206B etc.).

- The authors seem to have been "inspired" by the work of Huo, Yang, 2022 (https://doi.org/10.1016/j.bej.2022.108540), as the logic and structure of the introduction of the reviewed manuscript are similar to those of the referenced article. In addition, some phrases remained unchanged.

- Figure 4a: This scheme is exactly the same as Figure 4e from https://doi.org/10.1016/j.bej.2022.108540. Insert a citation in the figure caption.

- Materials and Methods. There is no information about metabolite identification. Please add analytical procedures.

- Supplemetary files folder contains wrong documents. Please resubmit the correct files.

Specific comments: 

- Descipher colours in the Figure 1d. 

Author Response

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Author Response File: Author Response.docx

Round 2

Reviewer 4 Report

Dear authors,

Thank you for the modifications that you have agreed to make following my suggestions.

However, please double check the Supplementary files you've resubmitted. There are no Figures S1–S2 and Tables S1–S7. There are only five main figures (Figures 1–5). Please pay attention to that.

Author Response

Dear Reviewer： 

（1）Please double check the Supplementary files you've resubmitted. There are no Figures S1–S2 and Tables S1–S7. There are only five main figures (Figures 1–5). Please pay attention to that.

I am very sorry about this problem. I have supplemented it according to your requirements and suggestions. For detailed instructions, please refer to supplementary materials. The supplementary material contains seven supplementary tables and four supplementary figures.

Table: 7

Table S1. Table S1. PCR specific primer sequence.

Table S2. Table S2. Physiological and biochemical characteristics of strain P1.

Table S3. Genomic characteristics of Pseudomonas sp. P1.

Table S4. Description of genes obtained from genome of P1 relevant to BPA degradation.

Table S5. Comparison of BPA degradation rates by various microorganisms

Table S6. Information about functional genes resistant to BPA toxicity.

Table S7 LC-MS data of BPA degradation intermediates

Figure: 4

Figure S1. Scanning electron microscope (A) and morphological observation (B) of strain P1.

Figure S2. The complete TCA cycle (A) and Benzoate degradation (B) were present in the genome of strain P1. The data are based on RAST analysis. Enzyme committee numbers were obtained from the KEGG database.

Figure S3. (A) PCR results of BPA degradation-related genes. (B) RT-PCR agarose gel electrophoresis of BPA degradation-related genes under different conditions.

Figure S4. Degradation of BPA by strain P1 (A) different temperature, (B) different pH, (C) different inoculum size, (D) different initial concentration.

Thank you again for your patient review and all the work you have done on our manuscript. Please correct me again if there is anything that needs further improvement.

Thank you and best regards.

Yours sincerely,

Shuaiguo Li

Author Response File: Author Response.doc