Complete Genome Report of a Hydrocarbon-Degrading Sphingobium yanoikuyae S72

Round 1

Reviewer 1 Report

The subject of the research was to determine the role of Sphingobium yanoikuyae S72 in the degradation of certain hydrocarbons.

In order to be printed, the manuscript must be carefully edited and the obtained experimental data statistically verified.

 Remarks

1.      The manuscript title should end in S72. Needless to say isolatetd from Mexico. Adequate geographic data in the Materials and Methods chapter is sufficient.

2.      Names of microorganisms should be italicized. The note applies to the entire manuscript.

3.      There are errors throughout the manuscript regarding the correct placement of spaces and indexes. This is the case, for example, in verses 91-94 and others.

4.      Line 99 - What fragment of genomic 16S rRNA was amplified?

5.      No information is provided in chapter 2 on how the data contained in Table 1 were obtained.

6.      Figures 1 and 2 data should be presented on the basis of regression equations.

7.      Figures 3, 4 and 5 are of poor quality.

8.      References chapter is not properly formatted.

9.      The first fragment of figure S2 is not very thorough.

10.   Figure S3 - The data on the arrows are not clear.

Author Response

Reviewer's comment: The manuscript title should end in S72. Needless to say isolated from Mexico. Adequate geographic data in the Materials and Methods chapter is sufficient.

Our response: we have removed the word "isolated from Mexico" from the title. 

Reviewer's comment: Names of microorganisms should be italicized. The note applies to the entire manuscript 

Our response: we have italicized the names of the microorganisms mentioned in the text. 

Reviewer's comment:  There are errors throughout the manuscript regarding the correct placement of spaces and indexes. This is the case, for example, in verses 91-94 and others.

 Our response: we have corrected these errors and have placed the spaces appropriately. 

Reviewer's comment:  Line 99 - What fragment of genomic 16S rRNA was amplified? 

Our response: we have corrected these errors and have placed the spaces appropriately. We have included in the text that about 1500 bp of 16S rRNA fragment was amplified.

Reviewer's comment: No information is provided in chapter 2 on how the data contained in Table 1 were obtained.

 Our response: API bacterial identification kit was used for the biochemical characterization of this strain and it was mentioned in the manuscript. As regard the method used for the characterization with kit, manufacturer's instruction was followed.

Reviewer's comment: Figures 1 and 2 data should be presented on the basis of regression equations.

Author's response: We would have loved to do this, but we do not have the tool for drawing a regression base graph. 

Reviewer's comment: Figures 3, 4, and 5 are of poor quality.

Author's response: They have been redrawn with very good quality.

Reviewer's comment: References chapter is not properly formatted.

Author's response: The references have been properly formatted. 

Reviewer's comment: the first fragment of figure S2 is not very thorough.

Author's response: We have adjusted it to give a thorough information

Reviewer's comment: Figure S3 - The data on the arrows are not clear. 

Author's response: We have adjusted the image so that the data can become visible. 

Reviewer 2 Report

The manuscript entitled "Complete genome report of a hydrocarbon degrading Sphingo- 2 bium yanoikuyae S72 isolated from Mexico" is an interesting investigation and complete genome sequencing of hydrocarbon degrading bacterial species can provide more insights in understanding the behavior of microbes behaviour during degradation process. The manuscript is interesting and can be accepted after addressing some minor comments

1. Check for english spelling and gramatical mistakes in the whole manuscript.

2. Some data can go in supplementary information for example table 3 and figure 3 as this information is not necessary in the main text.

3. Quality of figure 4 is very poor same is the case of figure 5.

4. Rewrite the conclusion section and give clear cut findings from your invetigation

Author Response

Reviewer's comment:  Check for English spelling and grammatical mistakes in the whole manuscript.

Author's response: One of us who is a native speaker has checked and corrected some English and grammatical errors in the text. 

Reviewer's comment: Some data can go in supplementary information for example table 3 and figure 3 as this information is not necessary in the main text.

Author's response: We have move table 3 to supplementary file and figure 3 wa s added to figure S2. 

Reviewer's comment: Quality of figure 4 is very poor same is the case of figure 5.

Author's response: The figures have been redrawn to give a better quality and resolution. 

Reviewer's comment:  Rewrite the conclusion section and give clear cut findings from your invetigation.

Author's response: We have rewritten the conclusion to give more information and summary of the findings in the study. 

Reviewer 3 Report

1. The work was carried out using previously isolated strain. The strain was reported only in the thesis entitled Caracterización de Sphingobium sp. Aislado de la rizósfera de sorgo y su posible papel en biodegradación, Reynosa, Mexico in 2014, reference cited in 2018 of the manuscript. Please clarify this.

2. Growth conditions for strains and media should be added to the MS with proper ingredients.

3. SD data is missing in biodegradation studies. Please add.

4. GCMS graphs are not clear. Please improve the resolution.

5. Include the enzymatic study and their potent role in biodegradation 

6. Clearly describe the experimental design in the Materials and Methods (Replicates)?

7. Please rewrite the discussion. Try to limit the content and compare the obtained data with previous data rather than unmeaningful.

Author Response

The work was carried out using previously isolated strain. The strain was reported only in the thesis entitled Caracterización de Sphingobium sp. Aislado de la rizósfera de sorgo y su posible papel en biodegradación, Reynosa, Mexico in 2014, reference cited in 2018 of the manuscript. Please clarify this.

Author's response: We have checked the citation and made the appropriate correction. 

2. Growth conditions for strains and media should be added to the MS with proper ingredients.

Author's response: We actually mentioned the condition of growth in BH medium such as growth at 30 degrees in a rotary shaker incubator

SD data is missing in biodegradation studies. Please add.

Author's response: We have added the SD data for the biodegradation studies 

GCMS graphs are not clear. Please improve the resolution.

Author's response: The graphs have been redrawn to give a better resolution.

 Include the enzymatic study and their potent role in biodegradation, 

Author's response: Unfortunately, we did not carry out the enzyme assay for the degradation study and as such we are unable to provide such information at the moment.  

Clearly, describe the experimental design in the Materials and Methods (Replicates)?

Author's response: We tried to clarify the material and method which will believe will be sufficient for experimental replication.

Please rewrite the discussion. Try to limit the content and compare the obtained data with previous data rather than unmeaningful.

Author's response: The discussion has been rewritten. 

Round 2

Reviewer 1 Report

The current version of the manuscript is better than the previous one. In my opinion, the manuscript is suitable for publication.

Reviewer 3 Report

From the drafting perspective and the contents of the MS, after revision, it looks well.