Peer Review History

Original SubmissionDecember 15, 2023
Decision Letter - Wajdy Jum’ah Al-Awaida, Editor

PONE-D-23-42265Integrated Water Quality Dynamics in Wadi Hanifah: Physical, Chemical, and Biological PerspectivesPLOS ONE

Dear Dr. Aqel,

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 Feb 23 2024 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.

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). You should upload this letter as a separate file labeled 'Response to Reviewers'.
  • A marked-up copy of your manuscript that highlights changes made to the original version. You should upload this as a separate file labeled 'Revised Manuscript with Track Changes'.
  • An unmarked version of your revised paper without tracked changes. You should upload this as a separate file labeled 'Manuscript'.

If you would like to make changes to your financial disclosure, please include your updated statement in your cover letter. Guidelines for resubmitting your figure files are available below the reviewer comments at the end of this letter.

If applicable, we recommend that you deposit your laboratory protocols in protocols.io to enhance the reproducibility of your results. Protocols.io assigns your protocol its own identifier (DOI) so that it can be cited independently in the future. For instructions see: https://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols. 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,

Wajdy Jum’ah Al-Awaida, Ph.D

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. We suggest you thoroughly copyedit your manuscript for language usage, spelling, and grammar. If you do not know anyone who can help you do this, you may wish to consider employing a professional scientific editing service.  

Whilst you may use any professional scientific editing service of your choice, PLOS has partnered with both American Journal Experts (AJE) and Editage to provide discounted services to PLOS authors. Both organizations have experience helping authors meet PLOS guidelines and can provide language editing, translation, manuscript formatting, and figure formatting to ensure your manuscript meets our submission guidelines. To take advantage of our partnership with AJE, visit the AJE website (http://learn.aje.com/plos/) for a 15% discount off AJE services. To take advantage of our partnership with Editage, visit the Editage website (www.editage.com) and enter referral code PLOSEDIT for a 15% discount off Editage services.  If the PLOS editorial team finds any language issues in text that either AJE or Editage has edited, the service provider will re-edit the text for free.

Upon resubmission, please provide the following: 

● The name of the colleague or the details of the professional service that edited your manuscript

● A copy of your manuscript showing your changes by either highlighting them or using track changes (uploaded as a *supporting information* file)

● A clean copy of the edited manuscript (uploaded as the new *manuscript* file)

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. We note that Figure 1 in your submission contain map/satellite images which may be copyrighted. All PLOS content is published under the Creative Commons Attribution License (CC BY 4.0), which means that the manuscript, images, and Supporting Information files will be freely available online, and any third party is permitted to access, download, copy, distribute, and use these materials in any way, even commercially, with proper attribution. For these reasons, we cannot publish previously copyrighted maps or satellite images created using proprietary data, such as Google software (Google Maps, Street View, and Earth). For more information, see our copyright guidelines: http://journals.plos.org/plosone/s/licenses-and-copyright.

We require you to either (a) present written permission from the copyright holder to publish these figures specifically under the CC BY 4.0 license, or (b) remove the figures from your submission:

a. You may seek permission from the original copyright holder of Figure 1 to publish the content specifically under the CC BY 4.0 license.  

We recommend that you contact the original copyright holder with the Content Permission Form (http://journals.plos.org/plosone/s/file?id=7c09/content-permission-form.pdf) and the following text:

“I request permission for the open-access journal PLOS ONE to publish XXX under the Creative Commons Attribution License (CCAL) CC BY 4.0 (http://creativecommons.org/licenses/by/4.0/). Please be aware that this license allows unrestricted use and distribution, even commercially, by third parties. Please reply and provide explicit written permission to publish XXX under a CC BY license and complete the attached form.”

Please upload the completed Content Permission Form or other proof of granted permissions as an "Other" file with your submission.

In the figure caption of the copyrighted figure, please include the following text: “Reprinted from [ref] under a CC BY license, with permission from [name of publisher], original copyright [original copyright year].”

b. If you are unable to obtain permission from the original copyright holder to publish these figures under the CC BY 4.0 license or if the copyright holder’s requirements are incompatible with the CC BY 4.0 license, please either i) remove the figure or ii) supply a replacement figure that complies with the CC BY 4.0 license. Please check copyright information on all replacement figures and update the figure caption with source information. If applicable, please specify in the figure caption text when a figure is similar but not identical to the original image and is therefore for illustrative purposes only.

The following resources for replacing copyrighted map figures may be helpful:

USGS National Map Viewer (public domain): http://viewer.nationalmap.gov/viewer/

The Gateway to Astronaut Photography of Earth (public domain): http://eol.jsc.nasa.gov/sseop/clickmap/

Maps at the CIA (public domain): https://www.cia.gov/library/publications/the-world-factbook/index.html and https://www.cia.gov/library/publications/cia-maps-publications/index.html

NASA Earth Observatory (public domain): http://earthobservatory.nasa.gov/

Landsat: http://landsat.visibleearth.nasa.gov/

USGS EROS (Earth Resources Observatory and Science (EROS) Center) (public domain): http://eros.usgs.gov/#

Natural Earth (public domain): http://www.naturalearthdata.com/

5. Please upload a copy of Figure 2, to which you refer in your text on page 11. If the figure is no longer to be included as part of the submission please remove all reference to it within the text.

Additional Editor Comments:

Dear Authers

After thoroughly reviewing the manuscript "Integrated Water Quality Dynamics in Wadi Hanifah: Physical, Chemical, and Biological Perspectives," I have identified several areas where the article could be significantly improved:

1. Inadequate Methodological Detail:

The description of the sampling methods and locations lacks sufficient detail, making it difficult to assess the replicability and rigor of the study.

The analytical techniques used for water quality assessment are not described in enough detail to evaluate their appropriateness or accuracy.

2. Data Presentation Issues:

The tables and figures, while present, are not effectively integrated into the text. Clearer references and explanations in the manuscript would better contextualize these visual aids.

The statistical analysis methods, if used, are not clearly outlined. There's a need for a more comprehensive explanation of the statistical methods and their rationale.

3. Weak Discussion and Conclusions:

The discussion lacks depth in comparing the findings with other studies or historical data. This limits the contextual understanding of the study's results.

The conclusions drawn are relatively generic and do not sufficiently encapsulate the specific findings of this study.

4. Lack of Broader Implications:

The manuscript does not adequately discuss the broader implications of its findings, particularly in relation to environmental management and policy.

5. Inconsistencies and Errors:

There are several inconsistencies in terminology and units of measurement, which can be confusing.

The manuscript contains grammatical and typographical errors that detract from its overall quality.

6. Limited Reference to Current Literature:

The references seem outdated or not sufficiently relevant to the study's focus, which raises questions about the thoroughness of the literature review.

7. Need for Additional Research Suggestions:

The study lacks suggestions for future research or fails to identify gaps in the current understanding that it addresses.

8. Ethical and Compliance Issues:

The manuscript does not clearly state ethical compliance related to sample collection, which is crucial for studies involving environmental sampling.

9. Funding and Conflict of Interest Statements:

The manuscript should include a clear statement regarding funding sources and any potential conflicts of interest.

In summary, while the manuscript provides valuable insights into the water quality of Wadi Hanifah, improvements in methodological clarity, data presentation, discussion depth, error correction, and literature contextualization are essential for enhancing its academic rigor and impact.

[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: Yes

Reviewer #2: Yes

**********

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 manuscript describes comprehensive evaluation of water quality in one of the known valleys in Arabian Peninsula of Saudi Arabia. Analysis included physical, Chemical constituents and bacterial contamination but did not discuss how the study's outcomes are different from the previous studies about the same valley. This point must be addressed carefully.

Reviewer #2: The author is required to follow the remarks provided in the report submitted to the journal editor, as these comments are essential for reaching a conclusive decision on whether to accept the publication of this article.

**********

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: Yes: Husni othman

**********

[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: reviewer comments.pdf
Revision 1

Subject: Response to Editorial and reviewer comments on Manuscript [PONE-D-23-42265]

Dear Dr. Al-Awaida,

Thank you for your letter regarding our manuscript entitled "[Manuscript Title]" submitted to PLOS ONE. We appreciate the opportunity to revise our manuscript and address the concerns raised by both you and the reviewers. We have carefully considered each point and have made appropriate revisions to the manuscript.

Revision in response to reviewer comments

We have addressed each of the specific comments made by the reviewers. Our responses are detailed in the attached 'Response to Reviewers' document. Here are some highlights of the revisions:

1. Introduction: Expanded details about the history and significance of Wadi Hanifa and how our study differs from previous investigations.

2. Materials and Methods: Provided more information on the selection of study locations, sample collection, and detailed descriptions of laboratory methods and principles.

3. Combine Results and Discussion

• Clarified the methodology for various tests and improved the presentation of data in tables and figures.

• Enhanced the depth of the discussion by comparing findings with other studies and addressed the implications of our findings.

Editorial comments and Journal requirements

1. Methodological details: We have provided additional details in the Methods section for better understanding and replicability of the study.

2. Data presentation: Revised tables and figures for better integration into the text and provided a clearer explanation of statistical methods used.

3. Discussion and Conclusions: Expanded the discussion section to provide more context and depth and refined the conclusions to be more specific to our findings.

4. Broader implications: Discussed the broader implications of our findings in relation to environmental management and policy.

5. Inconsistency and Errors: We have corrected all identified inconsistencies and errors.

6. Reference to current literature: Updated and expanded the list of references to include more relevant and recent studies.

7. Research suggestions and Ethical compliance: Included suggestions for future research and provided detailed information regarding ethical compliance.

8. Funding and conflict of interest statements: Updated the manuscript to include a clear statement regarding funding sources and any potential conflicts of interest.

9. Style and language editing: We have engaged a professional editing service to ensure that the manuscript meets PLOS ONE's style requirements and is free from language errors. The details of the service used, and the marked-up copy of the manuscript are included in the submission.

10. Figure copyright issues: We have addressed the concerns regarding Figure 1 by removing the figure.

11. Permits for field work: Included detailed information about the permits obtained for the study in the Methods section. (Lines 141-142)

We believe that these revisions address the concerns raised and significantly improve the manuscript. We hope that it now meets the publication criteria for PLOS ONE. We look forward to the opportunity to contribute to the journal.

1. Regarding Figure 1: We have already removed this figure from our manuscript, acknowledging the concerns regarding copyrighted maps or satellite images created using proprietary data.

2. Regarding S1 Figures: We would like to clarify that the S1 Figures are entirely original and do not require special permissions for publication under the CC BY 4.0 license. These images were captured by our research team directly from the collection sites. They are not sourced from any third-party proprietary software or databases, ensuring full compliance with the journal's copyright guidelines.

We hope this addresses your concerns satisfactorily. Please feel free to reach out if further clarification or action is needed.

Thank you for considering our work for publication in PLOS ONE. Please find the revised manuscript, along with the 'Response to Reviewers' document and other required items, attached.

Regards,

Hazem Aqel

Attachments
Attachment
Submitted filename: Response to Reviewer Comments.docx
Decision Letter - Wajdy Jum’ah Al-Awaida, Editor

Integrated Water Quality Dynamics in Wadi Hanifah: Physical, Chemical, and Biological Perspectives

PONE-D-23-42265R1

Dear Dr. Aqel,

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 for payment will follow shortly after the formal acceptance. To ensure an efficient process, please log into Editorial Manager at http://www.editorialmanager.com/pone/, click the 'Update My Information' link at the top of the page, and double check that your user information is up-to-date. If you have any billing related questions, 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,

Wajdy Jum’ah Al-Awaida, Ph.D

Academic Editor

PLOS ONE

Additional Editor Comments (optional):

Reviewers' comments:

Formally Accepted
Acceptance Letter - Wajdy Jum’ah Al-Awaida, Editor

PONE-D-23-42265R1

PLOS ONE

Dear Dr. Aqel,

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

Prof. Wajdy Jum’ah Al-Awaida

Academic Editor

PLOS ONE

Open letter on the publication of peer review reports

PLOS recognizes the benefits of transparency in the peer review process. Therefore, we enable the publication of all of the content of peer review and author responses alongside final, published articles. Reviewers remain anonymous, unless they choose to reveal their names.

We encourage other journals to join us in this initiative. We hope that our action inspires the community, including researchers, research funders, and research institutions, to recognize the benefits of published peer review reports for all parts of the research system.

Learn more at ASAPbio .