Comparative Genomic Analysis of Extracellular Electron Transfer in Bacteria

Round 1

Reviewer 1 Report

Comments and Suggestions for Authors

1. Organism names like Pseudomonas aeruginosa, Rhodobacter sphaeroides, Rhodopseudomonas palustris, Thermincola potens, Shewanella oneidensis, Geobacter metallireducens, and Geobacter sulfurreducens should be in italics. Authors need to check entire manuscript and corrections need to be made throughout the manuscript.

2. Either Fig or Figure need to be mentioned in the manuscript not both

3. Authors need to mention the mechanism of electron transport and principal involved in MFC

4. Authors mentioned about Microbial fuel cells in the abstract. It gives an impression that there is application of MFC in the manuscript. But the study is not directly related to MFC.  It would be good if the author mentioned the application at the end, rather than in the beginning.

5. If the manuscript is observed in the MFC perspective, no information is available in the manuscript.

6. Most of the references are old. Very few references are restricted up to 2021.  

7. Figures are not clear.

 

5.

 

2. 

Comments on the Quality of English Language

Quality of English language is good

Author Response

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Author Response File: Author Response.pdf

Reviewer 2 Report

Comments and Suggestions for Authors

This interesting work did comparative genomic analysis of bacteria’s extracellular electron transfer. The author compared showed the extracellular electron transfer characteristics of 85 genomes from 9 genera. Through detailed analysis, the authors found that 4 genera Desulfuromonas, Geobacter, Geothrix, and Shewanella have more extracellular electron transfer genes. This study provide a novel approach to investigating potential exoelectrogens in comparative genomes. The manuscript is interesting, well organized and well written with convincing results. Therefore, I recommend to accept in present form.

Author Response

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Author Response File: Author Response.pdf

Reviewer 3 Report

Comments and Suggestions for Authors

Strengths:

1. This study aims to apply computational approach to analyze the bacterial genomes on NCBI to identify the EET-related genes. The bacterial genomes were selected for those of complete assembly, and subjected to gene prediction and annotation, and search for EET genes for pangenome analysese. Multiple algorithms were adopted in the workflow, covering different aspects of the data analyses and also those of fragmented genes.
2. The broad genomic datasets and the use of multiple bioinformatics tools appear to serve a good foundation for the intended data mining for EET genes across the species spectrum.

 

Weakness:

1.       Lack of transcriptome data to go along in support of the result.

2.       No functional enrichment analysis and pathway analysis to support the implications.

3.       Lack of detailing the specific implications of clustering results, especially regarding MFC applications to strengthen the impact.

4.       Lack of description of the biological relevance of these genes within EET pathways for novelty.

5.       While the study emphasizes gene presence, it could benefit from tying gene functions more directly to MFC performance metrics if possible, e.g. discussing the known roles of specific genes in electricity generation or electron shuttling.

6.       Not much of new findings were obtained from the study. The conclusions derived at the end are already known in large.

 

Specific Qs and problems:

1.       The authors concluded that "66 genes in these bacteria were significantly higher than the other five bacteria (p<0.01) based on PEPPAN followed by Twilight analysis": does higher gene counts confer high capacity in electron transfer? Or more dynamic responses to diverse environments? (no promoter analyses? no RNA-seq?)

 

2.       Figure quality is very low, especially on the text part. Except for Figure1, all the text of other figures are undiscernible. Specifically, Fig.2 ANI Dendrogram is of way too low resolution and very fuzzy, and the text is unreadable. Fig. 3-5 are not much better. 

Author Response

Please see the attachment.

Author Response File: Author Response.pdf

Round 2

Reviewer 1 Report

Comments and Suggestions for Authors

Revised manuscript can be accepted.

Comments on the Quality of English Language

Quality of English is good

Author Response

Thank you for the positive comment. Regarding the English writing, we have the revised manuscript for English editing by MDPI's Author Services with the ID of english-86713. 

Best regards,

 

lin