Peer Review History
| Original SubmissionMay 20, 2025 |
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Dear Dr. Cap, 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. Please submit your revised manuscript by Sep 01 2025 11:59PM. If you will need more time than this to complete your revisions, please reply to this message or contact the journal office at plosone@plos.org . When you're ready to submit your revision, log on to https://www.editorialmanager.com/pone/ and select the 'Submissions Needing Revision' folder to locate your manuscript file.
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We note that you have provided funding information that is not currently declared in your Funding Statement. However, funding information should not appear in the Acknowledgments section or other areas of your manuscript. We will only publish funding information present in the Funding Statement section of the online submission form. Please remove any funding-related text from the manuscript and let us know how you would like to update your Funding Statement. Currently, your Funding Statement reads as follows: This study was funded by private funds from Rizobacter S.A. and public funds from the research project 2019-PE-E7-I120 of the National Institute of Agricultural Technology. Please include your amended statements within your cover letter; we will change the online submission form on your behalf. 5. Please amend your list of authors on the manuscript to ensure that each author is linked to an affiliation. 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Please remove all personal information, ensure that the data shared are in accordance with participant consent, and re-upload a fully anonymized data set. Note: spreadsheet columns with personal information must be removed and not hidden as all hidden columns will appear in the published file. Additional guidance on preparing raw data for publication can be found in our Data Policy (https://journals.plos.org/plosone/s/data-availability#loc-human-research-participant-data-and-other-sensitive-data) and in the following article: http://www.bmj.com/content/340/bmj.c181.long. 9. Please include captions for your Supporting Information files at the end of your manuscript, and update any in-text citations to match accordingly. Please see our Supporting Information guidelines for more information: http://journals.plos.org/plosone/s/supporting-information. [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? Reviewer #1: Yes Reviewer #2: Yes Reviewer #3: Yes ********** 2. Has the statistical analysis been performed appropriately and rigorously? -->?> Reviewer #1: I Don't Know Reviewer #2: Yes Reviewer #3: Yes ********** 3. Have the authors made all data underlying the findings in their manuscript fully available??> The PLOS Data policy Reviewer #1: Yes Reviewer #2: Yes Reviewer #3: Yes ********** 4. Is the manuscript presented in an intelligible fashion and written in standard English??> Reviewer #1: Yes Reviewer #2: No Reviewer #3: Yes ********** Reviewer #1: Greetings Dear authers, this manuscript evaluated the effectiveness of PMA-qPCR for quantifying viable Bradyrhizobium diazoefficiens in commercial inoculants. Kindly note: In methods you did not write the date or period of current study for example from May 2024 to December 2024.This is important scientifically. Kind regards. Reviewer #2: Abstract: Line 17 = Please clarify what is the meaning of "Approximately 95% efficiency", efficiency of what? qPCR amplification? Line 21= Discrimination threshold assessment” is vague — consider clarifying what this means (e.g., dilution sensitivity? detection limit? The abstract would benefit from aligning with a standard of scientific format: Background, Objective, Methods, Results, Conclusion/impact. Keywords could be expanded to better reflect the focus of the research. Introduction: Line 43-48 = The PMA explanation should be streamlined. Line 52-54 = the last sentence shifts to “we demonstrated…” this implies the authors of the current paper have already published this prior work. If not, please revise to clarify the authorship. Line 55-58 = Consider stronger emphasize for objective statement (ex: This study evaluates the use of PMA-qPCR to quantify viable Bradyrhizobium diazoefficiens in commercial inoculants, including assay optimization, PMA protocol refinement, and validation on finished products). Methods: Line 63 = Please indicate the type of diluent used for serial dilutions and the dilution range. Please specify what is the meaning of modified Mannitol Yeast Agar with Congo Red? Line 68 = Clarify the kit name, and add a brief info what kind of sample was used? Line 69 = manufacture instructions --> manufacturer's instructions Line 84 & Line 86 shows the redundancy of LOD, please consider to merge this statement for clarity. Line 91 = unclear phrasing "Samples were considered positive when Ct values were below 40" should be "Samples with Ct values below 40 were considered positive...." Line 103 = The “xx” should be replaced with the actual catalog number or information (e.g., PMAxx or PMA-Lite), or removed if unknown. Line 106 = "Briefly, 100 µl of PMA Enhancer...” Briefly” is often overused, it can be removed or replaced with more scientific phrasing (µl should consistently be written as “µL” (capital L), ml should be mL according to standard SI unit formatting). Line 107 = ".............. to the desired final concentration" is unclear, should be revised "...........to reach to final concentration of 50, 75, or 100 µM." Line 117 = analyze should be analyzed (use past tense throughout the method). Line 155 = lineal .....should be linear Line 158 = "For the latter...." is vague, consider for merging for clarity. Line 190-192 = The sentence would benefit from a brief contextual explanation (e.g., what mixture was tested, and whether viable cells were diluted in a constant background of non-viable cells). Consider defining the experimental condition: were the non-viable cells added at a fixed concentration? p should be italicized for publication style. Line 215 = “intra-assay repeatability and standard deviation of 0.3” should be “...with intra-assay repeatability indicated by a standard deviation of 0.3”. “an intra assay reproducibility” → should be “inter-assay reproducibility” based on context (between runs), and needs a hyphen in “inter-assay”. Line 243 = failed to distinguish should be more formal such as was unable to resolve Line 244 = "half strength ....... and quarter strength ....... " should be written as "half-strength and quarter-strength" Line 250 = "was able to determine the number of viable cells in only just 5 2 h" should be written as "...... in just 5.2 hours....." (make sure the decimal is accurate and consistent). Line 251 = " ....while maintaining an 82%....." is redundant with earlier sentence and could be omitted or restated more precisely. Line 265 = " some researchers ......" avoid vague phrases, change to be more precise Be consistent with species names (italicize Herbaspirillum seropedicae, Bradyrhizobium diazoefficiens). Reviewer #3: Major Comments 1. Methodological Clarity o PMA Optimization (Section 2.5.1): The manuscript states that 50 µM PMA was selected for subsequent assays but does not explicitly justify why this concentration was optimal (e.g., statistical comparison of inhibition efficacy across 50, 75, and 100 µM). Include a quantitative analysis (e.g., % signal inhibition at each concentration) to support this choice. o Heat Inactivation Controls: Clarify whether heat inactivation (95°C for 10 min) was validated to ensure complete cell death without DNA fragmentation, which could affect PMA binding efficiency. A viability stain (e.g., SYTOX Green) could corroborate this. 2. Statistical Analysis o Figure 2c (Experiment 4): The inability to distinguish 2-fold dilutions contrasts with the stated SD of 0.3 log CFU/mL. Reconcile this discrepancy by discussing technical limitations (e.g., pipetting error, PMA heterogeneity) or proposing a higher dilution factor for finer discrimination. o Regression Analysis (Figure 3a): The R² of 0.82 suggests unexplained variability. Discuss potential sources (e.g., matrix effects, PMA penetration variability) and how they might be mitigated in industrial applications. 3. Comparative Advantages o Time/Cost Savings: Emphasize the economic impact of reducing processing time from 120 h to 5 h. Include a brief cost comparison (e.g., reagents, labor) between PMA-qPCR and plate counting to highlight scalability. o VBNC State: The dismissal of VBNC cells (lines 259–261) lacks experimental evidence. Cite supporting data or reference prior studies showing cryoprotectants prevent VBNC formation in Bradyrhizobium. 4. Industrial Applicability o Sample Throughput: Describe how the method scales for high-throughput batch testing (e.g., number of samples processed per run, automation potential). o Matrix Variability: Address whether the method was tested across different inoculant formulations (e.g., peat-based vs. liquid carriers) to ensure broad applicability. Minor Comments 1. Abstract o Replace "82% correlation" with "R² = 0.82" for statistical precision. 2. Introduction o Line 52: Clarify how PMA’s nitrene radical binds DNA (covalent vs. intercalation) to aid reader understanding. 3. Results o Figure 1: Label axes in all panels (e.g., "Log CFU/mL" for bacterial counts). o Line 165: Specify which model (beta-Poisson or exponential) yielded the LOD of 3.14 log CFU/mL. 4. Discussion o Line 226: Expand on why LOD/LOQ values are acceptable despite being higher than other applications (e.g., inoculants typically have high cell densities). 5. References o Ensure all citations (e.g., Pedrolo et al., 2024) are in the bibliography. ********** 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 Reviewer #3: Yes: Maryam Zakavi ********** [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
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| Revision 1 |
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<p>PMA-qPCR: ACCELERATING THE MARKET RELEASE OF HIGH-QUALITY BRADYRHIZOBIUM DIAZOEFFICIENS INOCULANTS PONE-D-25-27271R1 Dear Dr. Cap, 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. For questions related to billing, please contact billing support . 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, Mohammad H. Ghazimoradi Academic Editor PLOS ONE Additional Editor Comments (optional): Reviewer #1: Reviewer #3: Reviewers' comments: Reviewer's Responses to Questions Comments to the Author Reviewer #1: All comments have been addressed Reviewer #3: All comments have been addressed ********** 2. Is the manuscript technically sound, and do the data support the conclusions??> Reviewer #1: Yes Reviewer #3: Yes ********** 3. Has the statistical analysis been performed appropriately and rigorously? -->?> Reviewer #1: Yes Reviewer #3: Yes ********** 4. Have the authors made all data underlying the findings in their manuscript fully available??> The PLOS Data policy Reviewer #1: Yes Reviewer #3: Yes ********** 5. Is the manuscript presented in an intelligible fashion and written in standard English??> Reviewer #1: Yes Reviewer #3: Yes ********** Reviewer #1: Greetings, The revisions have significantly improved the manuscript. It is now scientifically stronger and suitable for publication. Kind regards. Reviewer #3: Thank you for submitting your paper to PLOS One. Now all the comments have been addressed, and the manuscript could be accepted. ********** 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 #3: Yes: Maryam Zakavi ********** |
| Formally Accepted |
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PONE-D-25-27271R1 PLOS ONE Dear Dr. Cap, 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 You will receive further instructions from the production team, including instructions on how to review your proof when it is ready. Please keep in mind that we are working through a large volume of accepted articles, so please give us a few days 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. You will receive an invoice from PLOS for your publication fee after your manuscript has reached the completed accept phase. If you receive an email requesting payment before acceptance or for any other service, this may be a phishing scheme. Learn how to identify phishing emails and protect your accounts at https://explore.plos.org/phishing. 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. Mohammad H. Ghazimoradi Academic Editor PLOS ONE |
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