Proteogenomic Characterization of Pseudomonas veronii SM-20 Growing on Phenanthrene as Only Carbon and Energy Source

Round 1

Reviewer 1 Report

The article is devoted to the extensive investigation into the biodegradation capabilities and stress response of the newly isolated Pseudomonas veronii strain SM-20. The polycyclic aromatic hydrocarbon phenanthrene was studied as a model compound for biodegradation. Despite of the demonstrated efficiency of phenanthrene degradation by the strain studied was moderate (25% for 30 days at an initial PHE concentration of 0.6 g/l), authors applied modern approaches to sufficiently deeply and completely characterize both the metabolic pathways and mechanisms of stress-tolerance in bacteria P. veroni. Considering that bacteria of the genus Pseudomonas have long been widely studied as various pollutants degraders, authors justifiably presented the unique genomic and proteomic charactericteristics of a novel strain of P. veronii.

In my opinion, this manuscript may be published after minor revision concerning poor or erroneous spelling:

Line 595. “…bacteria like Rhizobacterium ensifer meliloti…” should be corrected as “…bacteria like Ensifer meliloti…”

Author Response

Dear Reviewer,

We are grateful for your positive assessment of our work and your acknowledgment of the significance of our findings. We appreciate your recognition of the modern approaches we applied to thoroughly characterize the metabolic pathways and stress-tolerance mechanisms of P. veronii, particularly in the context of phenanthrene degradation.

Regarding your suggestion concerning erroneous spelling, we want to assure you that our manuscript has been thoroughly proofread and edited for accuracy. The error in line 595 has been corrected to “…bacteria like Ensifer meliloti”

Thank you once again for dedicating your time and effort to reviewing our manuscript. We sincerely appreciate your constructive feedback.

Reviewer 2 Report

I have gone through the manuscript entitled “Proteogenomic characterization of Pseudomonas veronii SM-20 growing on phenanthrene as only carbon and energy source”. In this study, authors evaluated the potential of Pseudomonas veronii SM-20 for the degradation of phenanthrene. The study is well-designed, and the manuscript is properly written. The authors have conducted extensive and thorough work in this study. However, a minor revision would be beneficial for clarifying some aspects.

1. In section 3.3. authors refer to Figure 2 instead of Figure 3.

2. The authors identified the metabolic intermediates formed during PHE degradation by P. veronii. Did they analyze samples from different days during the biodegradation assay? It would be interesting to have information on the evolution of the metabolic intermediate profile over time, which could further support the scheme proposed in Figure 4

The overall quality of the English language in the manuscript is acceptable; however, minor editing is recommended to enhance clarity and coherence. Some sentences could benefit from a smoother flow and better organization of ideas.

Author Response

Dear Reviewer,

Thank you for your review of our manuscript. We appreciate your positive assessment of our study's design and thoroughness.

Regarding your first point, we acknowledge the error in referencing Figure 2 instead of Figure 3 in Section 3.3. We corrected it in the revised manuscript.

Regarding your second point, we are pleased to inform you that we did indeed analyze samples from different days (4, 7, 12, 15, 20, 25, and 30) during the biodegradation assay. However, only 9,10-phenanthrenequinone was detected after 20 days, and it was consistently observed until the end of the experiment. All other intermediates were detected on day 30th, as mentioned in the manuscript (lines 567-569), aligning with the information presented in Figure 4.

We also appreciate your feedback on the quality of English language. We want to assure you that our manuscript has been thoroughly proofread and edited using the services of a language editing professional to enhance clarity and coherence, ensuring a smoother flow.

Once again, thank you for dedicating your time and effort to reviewing our manuscript. We sincerely appreciate your constructive feedback.