Metabolic versatility and nitrate reduction pathways of a new thermophilic bacterium of the Deferrivibrionaceae: Deferrivibrio metallireducens sp. nov isolated from hot sediments of Vulcano Island, Italy

Grégoire  Galès; Mélanie Hennart; Maverick Hannoun; Anne Postec; Gaël Erauso

doi:10.1371/journal.pone.0315093

Peer Review History

Original SubmissionJuly 29, 2024
29 Jul 2024 Author Response https://doi.org/10.1371/journal.pone.0315093.r001
13 Sep 2024 Decision Letter - Vasu Appanna, Editor PONE-D-24-31234Metabolic versatility and nitrate reduction pathways of a new thermophilic bacterium of the Deferrivibrionaceae: Deferrivibrio metallireducens sp. nov isolated from hot sediments of Vulcano Island, ItalyPLOS ONE Dear Dr. GALES, Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we feel that it has merit but does not fully meet PLOS ONE’s publication criteria as it currently stands. Therefore, we invite you to submit a revised version of the manuscript that addresses the points raised during the review process.When you're ready to submit your revision Oct 28 2024 11:59PM, log on to https://www.editorialmanager.com/pone/ and select the 'Submissions Needing Revision' folder to locate your manuscript file. Please include the following items when submitting your revised manuscript: A rebuttal letter that responds to each point raised by the academic editor and reviewer(s). 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Additionally, PLOS ONE offers an option for publishing peer-reviewed Lab Protocol articles, which describe protocols hosted on protocols.io. Read more information on sharing protocols at https://plos.org/protocols?utm_medium=editorial-email&utm_source=authorletters&utm_campaign=protocols . We look forward to receiving your revised manuscript. Kind regards, Vasu D. Appanna Academic Editor PLOS ONE Journal requirements: When submitting your revision, we need you to address these additional requirements. 1. Please ensure that your manuscript meets PLOS ONE's style requirements, including those for file naming. The PLOS ONE style templates can be found at https://journals.plos.org/plosone/s/file?id=wjVg/PLOSOne_formatting_sample_main_body.pdf and https://journals.plos.org/plosone/s/file?id=ba62/PLOSOne_formatting_sample_title_authors_affiliations.pdf 2. Please include a complete copy of PLOS’ questionnaire on inclusivity in global research in your revised manuscript. Our policy for research in this area aims to improve transparency in the reporting of research performed outside of researchers’ own country or community. The policy applies to researchers who have travelled to a different country to conduct research, research with Indigenous populations or their lands, and research on cultural artefacts. The questionnaire can also be requested at the journal’s discretion for any other submissions, even if these conditions are not met. Please find more information on the policy and a link to download a blank copy of the questionnaire here: https://journals.plos.org/plosone/s/best-practices-in-research-reporting. Please upload a completed version of your questionnaire as Supporting Information when you resubmit your manuscript. 3. In your Methods section, please provide additional information regarding the permits you obtained for the work. Please ensure you have included the full name of the authority that approved the field site access and, if no permits were required, a brief statement explaining why. 4. Please include a separate caption for each figure in your manuscript. 5. Please review your reference list to ensure that it is complete and correct. If you have cited papers that have been retracted, please include the rationale for doing so in the manuscript text, or remove these references and replace them with relevant current references. Any changes to the reference list should be mentioned in the rebuttal letter that accompanies your revised manuscript. If you need to cite a retracted article, indicate the article’s retracted status in the References list and also include a citation and full reference for the retraction notice. Additional Editor Comments: Dear Dr. Gales Your manuscript titled "Metabolic versatility and nitrate reduction pathways of a new thermophilic bacterium of the Deferrivibrionaceae: Deferrivibrio metallireducens sp. nov isolated from hot sediments of Vulcano Island, Italy" has been reviewed and has been found acceptable for publication with minor revision. The work has revealed some interesting metabolic attributes of this thermophilic bacterium, however, it is important to limit the discussion section to the results obtained. Please take into account the suggestions of the reviewers in regard to the points raised while framing the revised version of the manuscript. Thank you Vasu D. Appanna PhD Professor [Note: HTML markup is below. Please do not edit.] Reviewers' comments: Reviewer's Responses to Questions Comments to the Author 1. Is the manuscript technically sound, and do the data support the conclusions? The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented. Reviewer #1: Yes Reviewer #2: Yes ******** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: N/A Reviewer #2: N/A ****** 3. Have the authors made all data underlying the findings in their manuscript fully available? The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified. Reviewer #1: Yes Reviewer #2: Yes ****** 4. Is the manuscript presented in an intelligible fashion and written in standard English? PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here. Reviewer #1: Yes Reviewer #2: Yes ******** 5. Review Comments to the Author Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters) Reviewer #1: The article by Grégoire et al. describes the isolation of a novel thermophilic bacterium. The manuscript is of interest, and the data support the conclusions. I only have minor recommendations: - Figure 6, FN graph: It is difficult to discern between the groups. Please change one to an open box or something more recognizable. - Figure 7: The X axis is cut off for cymA - Figure captions: What is your n value for the studies? Please list in figure captions (for all figures). For the TEM, was this a representative image? How many images were captured? - The Results and Discussion section is quite long (90 references) and contains a lot of hand-waving. For example, you discuss the roTCA cycle, and other enzymes that "could be" at work, but provide no functional evidence for many of them. I recommend trimming this section down by 2-3 pages and focusing on what was discovered and not what you believe may be happening Reviewer #2: Dear Editor, I have thoroughly reviewed the manuscript entitled "Metabolic versatility and nitrate reduction pathways of a new thermophilic bacterium of the Deferrivibrionaceae: Deferrivibrio metallireducens sp. nov. isolated from hot sediments of Vulcano Island, Italy," and I would like to offer the following comments for improvement: I have also mentined the some changes in the MS pdf. Please remove any unnecessary paragraphs from the abstract for better clarity. Ensure consistent formatting for temperature symbols (Celsius) throughout the manuscript. Properly align the tables and address any missing entries. Avoid the use of capitalized words inappropriately throughout the manuscript. Additionally, the manuscript requires English language corrections. Ensure proper referencing style and maintain consistency in the reference format. Italicize all scientific names and follow the standard rules of scientific nomenclature. In the Materials & Methods section, include the concentrations of the PCR components and provide details of the PCR programs used. Consider using iTOL tools for better representation of the phylogenetic analysis figure. Correct any grammatical and language errors throughout the manuscript. ******* 6. PLOS authors have the option to publish the peer review history of their article (what does this mean? ). If published, this will include your full peer review and any attached files. If you choose “no”, your identity will remain anonymous but your review may still be made public. Do you want your identity to be public for this peer review? For information about this choice, including consent withdrawal, please see our Privacy Policy . Reviewer #1: No Reviewer #2: No ******** [NOTE: If reviewer comments were submitted as an attachment file, they will be attached to this email and accessible via the submission site. Please log into your account, locate the manuscript record, and check for the action link "View Attachments". If this link does not appear, there are no attachment files.] While revising your submission, please upload your figure files to the Preflight Analysis and Conversion Engine (PACE) digital diagnostic tool, https://pacev2.apexcovantage.com/ . PACE helps ensure that figures meet PLOS requirements. To use PACE, you must first register as a user. Registration is free. Then, login and navigate to the UPLOAD tab, where you will find detailed instructions on how to use the tool. If you encounter any issues or have any questions when using PACE, please email PLOS at figures@plos.org . Please note that Supporting Information files do not need this step. Attachments Attachment Submitted filename: Reviewd 9.9.2024.pdf https://doi.org/10.1371/journal.pone.0315093.r002
Revision 1
28 Oct 2024 Author Response Dear Professor Appanna, I am grateful to you and the two reviewers for your contributions. As a result, we have improved the quality and relevance of our article. The publisher and the two reviewers were correct in noting that the results and discussion section was too long and speculative. We have reduced the article by two or three pages and withdrawn ten references. We have focused on what we can demonstrate and eliminated hand-waving. We are confident you will find the corrections to the manuscript convincing. You will find the answers to your questions and comments here, as well as in the text and figures. We have made the document easier to read by using bold and underlined text for our answers. 1. Please ensure that your manuscript meets PLOS ONE's style requirements, including those for file naming. The PLOS ONE style templates can be found at https://journals.plos.org/plosone/s/file?id=wjVg/PLOSOne_formatting_sample_main_body.pdf and https://journals.plos.org/plosone/s/file?id=ba62/PLOSOne_formatting_sample_title_authors_affiliations.pdf We have taken great care to ensure that the manuscript will meet your journal's expectations. 2. Please include a complete copy of PLOS’ questionnaire on inclusivity in global research in your revised manuscript. Our policy for research in this area aims to improve transparency in the reporting of research performed outside of researchers’ own country or community. The policy applies to researchers who have travelled to a different country to conduct research, research with Indigenous populations or their lands, and research on cultural artefacts. The questionnaire can also be requested at the journal’s discretion for any other submissions, even if these conditions are not met. Please find more information on the policy and a link to download a blank copy of the questionnaire here: https://journals.plos.org/plosone/s/best-practices-in-research-reporting. Please upload a completed version of your questionnaire as Supporting Information when you resubmit your manuscript. This section is irrelevant to our manuscript. We simply benefited from the help of Italian colleagues, who are mentioned in the acknowledgments. 3. In your Methods section, please provide additional information regarding the permits you obtained for the work. Please ensure you have included the full name of the authority that approved the field site access and, if no permits were required, a brief statement explaining why. No permits were required, as Italy is not a signatory to the Nagoya Protocol. We introduced the M&M section by saying: “Although Italy is not a signatory to the Nagoya Protocol, we carried out the sampling with the authorization of our collaborators from the INGV Palermo (Italy), as stated in the acknowledgments.” Indeed, we (Galès, Postec & Erauso) published last year a strain characterization in IJSEM from comparable samples:” Marinitoga aeolica sp. nov., a novel thermophilic anaerobic heterotroph isolated from a shallow hydrothermal field of Panarea Island in the Aeolian archipelago, Italy.” 4. Please include a separate caption for each figure in your manuscript. It has been done. 5. Please review your reference list to ensure that it is complete and correct. If you have cited papers that have been retracted, please include the rationale for doing so in the manuscript text, or remove these references and replace them with relevant current references. Any changes to the reference list should be mentioned in the rebuttal letter that accompanies your revised manuscript. If you need to cite a retracted article, indicate the article’s retracted status in the References list and also include a citation and full reference for the retraction notice. It has been done. No cited article has been retracted yet. As requested by the first reviewer, we have reduced the list of references (ten references withdrawn). Reviewer #1: The article by Grégoire et al. describes the isolation of a novel thermophilic bacterium. The manuscript is of interest, and the data support the conclusions. I only have minor recommendations: - Figure 6, FN graph: It is difficult to discern between the groups. Please change one to an open box or something more recognizable. It has been done. Nitrate is shown in an open box. This makes the figure easier to understand. - Figure 7: The X axis is cut off for cymA It has been corrected. - Figure captions: What is your n value for the studies? Please list in figure captions (for all figures). For the TEM, was this a representative image? How many images were captured? All experiments were performed in triplicate. About 25 TEM images were taken, from which we selected Figure 3. For the RT-qPCR experiments, three dilutions were analyzed. These clarifications have been included in the text and figure legends. - The Results and Discussion section is quite long (90 references) and contains a lot of hand-waving. For example, you discuss the roTCA cycle, and other enzymes that “could be” at work, but provide no functional evidence for many of them. I recommend trimming this section down by 2-3 pages and focusing on what was discovered and not what you believe may be happening The Results and Discussion section has been significantly reduced, as the reviewer asked. We have removed all sections deemed too speculative. The relevant section is now more than two pages shorter than initially planned, which improves the manuscript. Ten references have been withdrawn. We have eliminated the lengthy discussion of the roTCA cycle and the denitrification/DNRA switch regulation, which will be the subject of further research. Reviewer #2: Dear Editor, I have thoroughly reviewed the manuscript entitled "Metabolic versatility and nitrate reduction pathways of a new thermophilic bacterium of the Deferrivibrionaceae: Deferrivibrio metallireducens sp. nov. isolated from hot sediments of Vulcano Island, Italy," and I would like to offer the following comments for improvement: I have also mentined the some changes in the MS pdf. Please remove any unnecessary paragraphs from the abstract for better clarity. There have been none in accordance with the wishes of the first reviewer. Ensure consistent formatting for temperature symbols (Celsius) throughout the manuscript. It has been done throughout the text. Properly align the tables and address any missing entries. This has been done. Avoid the use of capitalized words inappropriately throughout the manuscript. Additionally, the manuscript requires English language corrections. This has been corrected. Ensure proper referencing style and maintain consistency in the reference format. This has been done. Italicize all scientific names and follow the standard rules of scientific nomenclature. This has been done. In the Materials & Methods section, include the concentrations of the PCR components and provide details of the PCR programs used. This has been done. In the text: “Quantitative PCR was performed with 2 L cDNA (directly reverse transcribed DNA and 10-1/10-2 dilutions), 0.25 L of each 10 M primer, 10 L of 2X SyberGreen and 7.5 L of ultrapure RNAse/DNAse-Free distilled water (Thermofisher). Thermal cycling conditions were as follows: 2 min at 98°C, followed by 30 cycles of 5 s at 98°C, 30 s at 61°C, and 20 s at 72°C. Data collection was performed during each annealing phase.” Consider using iTOL tools for better representation of the phylogenetic analysis figure. Thank you for your valuable feedback regarding the phylogenetic analysis figures. We want to clarify that the phylogenetic trees presented in Figures 1 and 2 have already been generated using iTOL. To enhance clarity and provide a more detailed response to the reviewer, we have updated the legends for both figures accordingly. Correct any grammatical and language errors throughout the manuscript. This has been done, we hope our efforts will be seen and appreciated. We hope you will enjoy reading the corrections to this article. If you have any questions, please don’t hesitate to contact us. The corresponding authors Grégoire Galès gregoire.gales@univ-amu.fr Gaël Erauso gael.erauso@univ-amu.fr Attachments Attachment Submitted filename: Rebuttal_Letter_PlosOne.docx* https://doi.org/10.1371/journal.pone.0315093.r003
21 Nov 2024 Decision Letter - Vasu Appanna, Editor Metabolic versatility and nitrate reduction pathways of a new thermophilic bacterium of the Deferrivibrionaceae: Deferrivibrio metallireducens sp. nov isolated from hot sediments of Vulcano Island, Italy PONE-D-24-31234R1 Dear Dr. Gales We’re pleased to inform you that your manuscript has been judged scientifically suitable for publication and will be formally accepted for publication once it meets all outstanding technical requirements. Within one week, you’ll receive an e-mail detailing the required amendments. When these have been addressed, you’ll receive a formal acceptance letter and your manuscript will be scheduled for publication. An invoice will be generated when your article is formally accepted. Please note, if your institution has a publishing partnership with PLOS and your article meets the relevant criteria, all or part of your publication costs will be covered. Please make sure your user information is up-to-date by logging into Editorial Manager at Editorial Manager® and clicking the ‘Update My Information' link at the top of the page. If you have any questions relating to publication charges, please contact our Author Billing department directly at authorbilling@plos.org. If your institution or institutions have a press office, please notify them about your upcoming paper to help maximize its impact. If they’ll be preparing press materials, please inform our press team as soon as possible -- no later than 48 hours after receiving the formal acceptance. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information, please contact onepress@plos.org. Kind regards, Vasu D. Appanna Academic Editor PLOS ONE Additional Editor Comments (optional): Reviewers' comments: Reviewer's Responses to Questions Comments to the Author 1. If the authors have adequately addressed your comments raised in a previous round of review and you feel that this manuscript is now acceptable for publication, you may indicate that here to bypass the “Comments to the Author” section, enter your conflict of interest statement in the “Confidential to Editor” section, and submit your "Accept" recommendation. Reviewer #1: All comments have been addressed ******** 2. Is the manuscript technically sound, and do the data support the conclusions? The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented. Reviewer #1: (No Response) ****** 3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: (No Response) ****** 4. Have the authors made all data underlying the findings in their manuscript fully available? The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified. Reviewer #1: (No Response) ****** 5. Is the manuscript presented in an intelligible fashion and written in standard English? PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here. Reviewer #1: (No Response) ****** 6. Review Comments to the Author Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters) Reviewer #1: (No Response) ****** 7. PLOS authors have the option to publish the peer review history of their article (what does this mean? ). If published, this will include your full peer review and any attached files. If you choose “no”, your identity will remain anonymous but your review may still be made public. Do you want your identity to be public for this peer review? For information about this choice, including consent withdrawal, please see our Privacy Policy . Reviewer #1: No ******** https://doi.org/10.1371/journal.pone.0315093.r004
Formally Accepted
Acceptance Letter - Vasu Appanna, Editor PONE-D-24-31234R1 PLOS ONE Dear Dr. Grégoire, I'm pleased to inform you that your manuscript has been deemed suitable for publication in PLOS ONE. Congratulations! Your manuscript is now being handed over to our production team. At this stage, our production department will prepare your paper for publication. This includes ensuring the following: * All references, tables, and figures are properly cited * All relevant supporting information is included in the manuscript submission, * There are no issues that prevent the paper from being properly typeset If revisions are needed, the production department will contact you directly to resolve them. If no revisions are needed, you will receive an email when the publication date has been set. At this time, we do not offer pre-publication proofs to authors during production of the accepted work. Please keep in mind that we are working through a large volume of accepted articles, so please give us a few weeks to review your paper and let you know the next and final steps. Lastly, if your institution or institutions have a press office, please let them know about your upcoming paper now to help maximize its impact. If they'll be preparing press materials, please inform our press team within the next 48 hours. Your manuscript will remain under strict press embargo until 2 pm Eastern Time on the date of publication. For more information, please contact onepress@plos.org. If we can help with anything else, please email us at customercare@plos.org. Thank you for submitting your work to PLOS ONE and supporting open access. Kind regards, PLOS ONE Editorial Office Staff on behalf of Dr. Vasu D. Appanna Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0315093.r005

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