Biochemical response of Sonneratia alba Sm. branches infested by a wood boring moth (Gazi Bay, Kenya)

Elisha Mrabu Jenoh; Mohamed Traoré; Charles Kosore; Nico Koedam

doi:10.1371/journal.pone.0259261

Peer Review History

Original SubmissionJune 21, 2021
19 Aug 2021 Decision Letter - Mohammad Shahid, Editor PONE-D-21-20278 Biochemical response of Sonneratia alba Sm. branches infested by a wood boring moth (Gazi Bay, Kenya) PLOS ONE Dear Dr. Jenoh, 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 30 2021 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: http://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, Mohammad Shahid, 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. Thank you for stating the following in the Acknowledgments Section of your manuscript: “This research was funded by the Flemish Interuniversity Council—University Development Cooperation (VLIR-UOS; http://www.vliruos.be/) ICP Ph. D Scholarship 2011. The funder had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript” We note that you have provided funding information within the Acknowledgements Section. Please note that 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 research was funded by the Flemish Interuniversity Council—University Development Cooperation (VLIR-UOS; http://www.vliruos.be/)ICP Ph. D Scholarship 2011. The funder had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.” Please include your amended statements within your cover letter; we will change the online submission form on your behalf. 3. We note that you have stated that you will provide repository information for your data at acceptance. Should your manuscript be accepted for publication, we will hold it until you provide the relevant accession numbers or DOIs necessary to access your data. If you wish to make changes to your Data Availability statement, please describe these changes in your cover letter and we will update your Data Availability statement to reflect the information you provide. 4. Please note that in order to use the direct billing option the corresponding author must be affiliated with the chosen institute. Please either amend your manuscript to change the affiliation or corresponding author, or email us at plosone@plos.org with a request to remove this option. 5. We note that Figure 1 in your submission contain map 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 (1) present written permission from the copyright holder to publish these figures specifically under the CC BY 4.0 license, or (2) 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/ 6. We note that Figure 2 in your submission contain copyrighted images. 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 more information, see our copyright guidelines: http://journals.plos.org/plosone/s/licenses-and-copyright. We require you to either (1) present written permission from the copyright holder to publish these figures specifically under the CC BY 4.0 license, or (2) remove the figures from your submission: a. You may seek permission from the original copyright holder of Figure 2 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. [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: Partly Reviewer #2: Partly ******** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes Reviewer #2: No ****** 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: No 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: Sonneratia alba (S. alba) is an important mangrove plant grown in low intertidal zones of downstream estuarine systems of East Africa, Southeast Asia, northern Australia, Borneo and Pacific Islands, etc. The optimal growth of this plant reaches 5 to 50% seawater, indicating its capacity to tolerate high salinity and hypoxia. In this way, S. alba is ecologically significantly important. The infestation by a lepidopteran moth wood borer species is causing mortality of S. alba and create a huge ecological and economic loss. In this aspect, the topic of the present manuscript is very important and is a need of the current situation. Hence, I think the authors bring up some important issues that will spark considerable debate. However, the manuscript needs some changes and justification, which should be addressed to improve the quality of the paper. I do recommend this manuscript to be published in "Plos One" with major revision and the author/s need to address below comments/suggestions: 1. The work of the present manuscript is focused on the mangrove tree Sonneratia alba, having huge ecological importance. At the beginning of the introduction, the authors mentioned the name of the plant; however, the name of the family is missing. Here, authors need to mention it at an appropriate place because with the plant's name, giving its family name is essential. 2. In the section “Sampling sites and samples,” the authors collected samples from different ages of plants. In certain groups (i.e., A and C), the age of the plants is mentioned, while in the group B and D age of the plants is not given. Here, the authors need to mention the age of all plants. 3. In the material and method section, the author did not mention the time (month and year) of the sampling. The authors need to mention it. 4. It is a well-established fact that in plants, the lignin content varies with the age of the plants. In this manuscript, authors mentioned that lignin content plays a significant role in recovery and damaging from infestation. Hence, authors need to justify the results as they collected samples from different age plants. 5. In Fig. 3, i.e., FTIR spectrum, the authors need to mention the functional groups corresponding to each of the FTIR ranges. 6. The language of the manuscript is poor, and lots of grammatical and typo errors have been seen throughout the manuscript. Authors need to check and reframe the sentences critically. Reviewer #2: The article entitled "Biochemical response of Sonneratia alba Sm. branches infested by a wood boring moth (Gazi Bay, Kenya)" should be revised well upon the follwoing: 1- English Editing should be peformed 2- Statistical analysis should be more clear that represents the data collected 3- Refrances should be arranged as PLOS ONE style ****** 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: Yes:** Mantasha I. Department of Bio-Molecular Sciences, University of Mississippi, MS, USA 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. https://doi.org/10.1371/journal.pone.0259261.r001
Revision 1
1 Oct 2021 Author Response Dear Editor, I wish to resubmit our manuscript titled biochemical response of Sonneratia alba Sm. branches infested by a wood boring moth (Gazi Bay, Kenya). We have considered all the required changes suggested by the two reviews as much as it is possible. Below is the list the reviewers asked (in blue fonts) and our reaction towards the raised concerns (in Red fonts). A bout Fig. 1 and Fig. 2, The map layer has been well referenced to Kenya Marine and Fisheries Research Institute (KMFRI). This is a governmental research institute where I am an employee. Being an employee I have full rights to use the map layers as long as I acknowledge it on the map. Which I have done. AS for Fig. 2, I wish to say that this is my figure and thus no permission is needed for me to use it. Reviewer Comments Reviewer #1: Sonneratia alba (S. alba) is an important mangrove plant grown in low intertidal zones of downstream estuarine systems of East Africa, Southeast Asia, northern Australia, Borneo and Pacific Islands, etc. The optimal growth of this plant reaches 5 to 50% seawater, indicating its capacity to tolerate high salinity and hypoxia. In this way, S. alba is ecologically significantly important. The infestation by a lepidopteran moth wood borer species is causing mortality of S. alba and create a huge ecological and economic loss. In this aspect, the topic of the present manuscript is very important and is a need of the current situation. Hence, I think the authors bring up some important issues that will spark considerable debate. ***However, the manuscript needs some changes and justification, which should be addressed to improve the quality of the paper. I do recommend this manuscript to be published in "Plos One" with major revision and the author/s need to address below comments/suggestions: 1. The work of the present manuscript is focused on the mangrove tree Sonneratia alba, having huge ecological importance. At the beginning of the introduction, the authors mentioned the name of the plant; however, the name of the family is missing. Here, authors need to mention it at an appropriate place because with the plant's name, giving its family name is essential. Response: This has been done (see line 43) 2. In the section “Sampling sites and samples,” the authors collected samples from different ages of plants. In certain groups (i.e., A and C), the age of the plants is mentioned, while in the group B and D age of the plants is not given. Here, the authors need to mention the age of all plants. Response: It is true that the age of the trees at some of the plots have been given in the materials and methods section whereas other plots (B and D) have not been given. The reason for this is actually given in the materials and method section where the description of the sampling plots was given. Plot B and D are natural forest that have been since time immemorial whereas plot A and C are plantation. Thus information about these two plots is available. On the other hand, in this research, as indicated in the manuscript, all efforts were done to ensure the samples were taken from the same canopy height and the branches were of similar size as much as possible. Also it is difficult to give the general age of mangrove trees using readily available tools in plant science. This is because methods of age estimation in mangrove have not been fully developed as is the case in other trees in terrestrial forest. It is our belief that even providing the DBH does not add any scientific relevance since a fully grown mangrove may stagnant at some stage. 3. In the material and method section, the author did not mention the time (month and year) of the sampling. The authors need to mention it. Response: This has been done as requested (see lines 115-116) 4. It is a well-established fact that in plants, the lignin content varies with the age of the plants. In this manuscript, authors mentioned that lignin content plays a significant role in recovery and damaging from infestation. Hence, authors need to justify the results as they collected samples from different age plants. Response: As much as the samples were collected from trees of various ages, the number of cumulative samples was made large enough and equal between the three categories i.e. (Dead, recovered and control). To ensure lack of bias, it has been mentioned in the manuscript that all effort was put to ensure that sampled branches were taken from same canopy position and of similar size in every sampled tree. Thus the sampled branches were assumed to be of similar physiological and developmental processes in each sampled tree. The concluded results were therefore out of the influence of age and size due to the replication effect. 5. In Fig. 3, i.e., FTIR spectrum, the authors need to mention the functional groups corresponding to each of the FTIR ranges. Response: This suggestion has been considered. See new version of Fig 3. 6. The language of the manuscript is poor, and lots of grammatical and typo errors have been seen throughout the manuscript. Authors need to check and reframe the sentences critically. Response: We have thoroughly revised the manuscript and made many corrections, as can be observed in the Changes marked version of the revised manuscript. Reviewer #2: The article entitled "Biochemical response of Sonneratia alba Sm. branches infested by a wood boring moth (Gazi Bay, Kenya)" should be revised well upon the follwoing: 1- English Editing should be performed Response: We have thoroughly revised the manuscript and made many corrections, as can be observed in the Changes marked version of the revised manuscript. 2- Statistical analysis should be more clear that represents the data collected Response: this comment from the reviewer seems not clear from our opinion. However, we would like to mention that the statistical methods applied in this paper (PCA and LDA) are very commonly used methods for such research work. Furthermore, the coherence in the results is reflected by the fact that the results of PCA and LDA support each other. In addition, we applied the One-way ANOVA test to assess the statistical significance of the results. 3- Refrances should be arranged as PLOS ONE style Response: This suggestion has also been considered according to the journal requirements. We re-submit this work after carefully considering all the comments of the reviewers and having done the necessary changes. We once again submit that this work has not been prior submitted to any other journal for publication consideration. On behalf of all authors, Elisha Mrabu Jenoh Kenya Marine and Fisheries Research Institute P. O. Box 81651 (80100) Mombasa Kenya E-mail: elishamrabu@gmail.com or emrabu@kmfri.co.ke Attachments Attachment Submitted filename: Response to Reviewers.docx https://doi.org/10.1371/journal.pone.0259261.r002
18 Oct 2021 Decision Letter - Mohammad Shahid, Editor Biochemical response of Sonneratia alba Sm. branches infested by a wood boring moth (Gazi Bay, Kenya) PONE-D-21-20278R1 Dear Dr. Jenoh, 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, Mohammad Shahid, Ph.D. 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 Reviewer #2: 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: Yes Reviewer #2: Partly ****** 3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes Reviewer #2: Yes ****** 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: Yes Reviewer #2: Yes ****** 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: Yes Reviewer #2: Yes ****** 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: Journal- PLOS ONE Manuscript ID- PONE-D-21-20278 Title- Biochemical response of Sonneratia alba Sm. branches infested by a wood boring moth (Gazi Bay, Kenya) Dear Editor, Authors have fulfilled all the queries/comments as it was asked by reviewers previously. Hence, now the manuscript is well written. I believe that it is a nice piece of work for being published in the PLOS ONE. Finally, I recommend that the paper should be accepted for the publication in the present form. Decision- Accept Reviewer #2: (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 Reviewer #2: No https://doi.org/10.1371/journal.pone.0259261.r003
Formally Accepted
22 Oct 2021 Acceptance Letter - Mohammad Shahid, Editor PONE-D-21-20278R1 Biochemical response of Sonneratia alba Sm. branches infested by a wood boring moth (Gazi Bay, Kenya) Dear Dr. Jenoh: I'm pleased to inform you that your manuscript has been deemed suitable for publication in PLOS ONE. Congratulations! Your manuscript is now with our production department. 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 plosone@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 Shahid Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0259261.r004

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 .