Know your enemy: Application of ATR-FTIR spectroscopy to invasive species control

Claire Anne Holden; John Paul Bailey; Jane Elizabeth Taylor; Frank Martin; Paul Beckett; Martin McAinsh

doi:10.1371/journal.pone.0261742

Peer Review History

Original SubmissionOctober 19, 2021
26 Nov 2021 Decision Letter - Du Changwen, Editor PONE-D-21-33488Know your enemy: Application of ATR-FTIR spectroscopy to invasive species controlPLOS ONE Dear Dr. Holden, 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 Jan 10 2022 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 will change the online submission form on your behalf. 4. Thank you for stating the following in the Acknowledgments Section of your manuscript: "CAH is a member of the Centre for Global Eco-Innovation that is funded by the European Union Regional Development Fund and mediates the collaboration between Lancaster University and Phlorum Ltd. The authors declare that there is no conflict of interest." 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: "CAH is a member of the Centre for Global Eco-Innovation that is funded by the European Union Regional Development Fund and mediates the collaboration between Lancaster University and Phlorum Ltd. PB, of Phlorum Ltd, provided funding for CAH's studentship and expertise in Japanese Knotweed. " Please include your amended statements within your cover letter; we will change the online submission form on your behalf. Additional Editor Comments: The method made sense for the species discrimination, and the Reviwere gave a positive conment, I totally agree, I have gone through the manuscript, and some concerns raised as follwing: 1. The leaf samples are fresh or dry? is there pretreatment? 2. How to keep consistent contact without pressure in the FTIR-ATR recording? 3. In the materials and methods section, the wavenuber range is 4-4000 cm-1, but Figure 1 showes the range of 900-1800cm-1, how to confirm that this range is sufficient? how about other range? 4. Figure ciations should include more details. Such as , Figure 1, waht is the algorithm of spectra pre-processing? wavenumber range should be noted in Figure 2 and Figure 3. 5. Language problems should be considered, and language expression are sugested to be thorough checked and revised by native english speaker. [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 ******** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: 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 ****** 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 ****** 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 entitled "Know your enemy: Application of ATR-FTIR spectroscopy to invasive species control" addresses a relevant topic, that of the rapid identification of different species of invasive herbs, using the technique of vibrational FTIR spectroscopy. I am of the opinion that it should be accepted for publication after introducing the suggested corrections below. Corrections needed: line 19 - The only taxonomic categories that can be written in italics are genus, species, and categories below them. line 22 - Indicate the species name (note: Indicating the name of varieties without first indicating the name of the species is not taxonomically correct!) line 23 - Indicate the species name (note: Indicating the name of varieties without first indicating the name of the species is not taxonomically correct!) line 24 - The only taxonomic categories that can be written in italics are genus, species, and categories below them. line 28 - The same as line 22 and 23 line 60 - In each paragraph, the authors must always indicate the extensive and complete form of the names of the plants studied, so they should not limit themselves to indicating the initial letter "R." line 65 - The abbreviation "var." must not be written in italics line 277 - "compacta" and "japonica" in italics, please line 297 - The only taxonomic categories that can be written in italics are genus, species, and categories below them. line 306 - "compacta" and "japonica" in italics, please line 308 - The same as in line 306 line 321 - The same as in line 306 line 416 - The abbreviation "var." must not be written in italics line 429 - The only taxonomic categories that can be written in italics are genus, species, and categories below them. line 436 - "Motschulsky" is the name of the species authority, so is not written in italics line 449 - The only taxonomic categories that can be written in italics are genus, species, and categories below them. ****** 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:** Leonel Pereira [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.0261742.r001
Revision 1
2 Dec 2021 Author Response Response to Reviewers We thank Professor Leonel Pereira and Professor Du Changwen for their positive and constructive response to our manuscript and for their valuable comments as to how the submission can be improved still further. We welcome the opportunity to respond to each of the comments below. Changes made to the manuscript in response to the reviewer’s comments are tracked in word in the revised submission. Reviewer One - Professor Leonel Pereira line 19 - The only taxonomic categories that can be written in italics are genus, species, and categories below them. Italics have been removed from ‘Polygonaceae’. line 22 - Indicate the species name (note: Indicating the name of varieties without first indicating the name of the species is not taxonomically correct!) ‘Reynoutria’ has been added. line 23 - Indicate the species name (note: Indicating the name of varieties without first indicating the name of the species is not taxonomically correct!) ‘Reynoutria’ has been added. line 24 - The only taxonomic categories that can be written in italics are genus, species, and categories below them. Italics have been removed from ‘Polygonaceae’. line 28 - The same as line 22 and 23 ‘Reynoutria’ has been added to both mentions. line 60 - In each paragraph, the authors must always indicate the extensive and complete form of the names of the plants studied, so they should not limit themselves to indicating the initial letter "R." We have expanded all abbreviations of R. to Reynoutria, and F. to Fallopia. line 65 - The abbreviation "var." must not be written in italics Italics have been removed from ‘var’. line 277 - "compacta" and "japonica" in italics, please Italics have been added. line 297 - The only taxonomic categories that can be written in italics are genus, species, and categories below them. Italics have been removed from ‘Polygonaceae’. line 306 - "compacta" and "japonica" in italics, please Italics have been added. line 308 - The same as in line 306 Italics have been added. line 321 - The same as in line 306 Italics have been added. line 416 - The abbreviation "var." must not be written in italics Italics have been removed from ‘var’. line 429 - The only taxonomic categories that can be written in italics are genus, species, and categories below them. Italics have been removed from ‘Polygonaceae’. line 436 - "Motschulsky" is the name of the species authority, so is not written in italics Italics have been removed from ‘Motschulsky’. line 449 - The only taxonomic categories that can be written in italics are genus, species, and categories below them. Italics have been removed from ‘Polygonaceae’. Additional Editor Comments - Professor Du Changwen ‘The leaf samples are fresh or dry? is there pre-treatment?’ The following sentence has been added to the materials and methods, line 120: ‘Leaves were air-dried at the time of collection and subsequently stored in cardboard folders within purpose-built cupboards to protect them from light exposure.’ ‘How to keep consistent contact without pressure in the FTIR-ATR recording?’ Consistent contact was maintained by raising the leaf material mounted on a slide to meet the internal reflection element using a moving platform, as described in lines 138-140. ‘In the materials and methods section, the wavenumber range is 4-4000 cm-1, but Figure 1 shows the range of 900-1800 cm-1, how to confirm that this range is sufficient? how about other range?’ An explanation of this choice and an acknowledgement of other available options has been added to the discussion section, lines 403-412. ‘In the present study, the fingerprint region (1800–900 cm− 1) of acquired spectra was selected for chemometric analysis because biological molecules preferentially absorb light of these wavenumbers, including important biological absorptions due to lipids, proteins, carbohydrates, nucleic acids and protein phosphorylation [26]. Isolation of this fingerprint region (1800–900 cm− 1) has achieved good results in other plant studies [29,39,40,73–75], though the high region (3700-2800 cm–1) has also yielded valuable information in a range of applications [76–79] since it contains additional biologically relevant absorbances such as those for water (~3275 cm–1), protein (~3132 cm-1), fatty acids and lipids (~3005, ~2970, ~2942 and ~2855 cm–1) [26]. ‘Figure citations should include more details. Such as, Figure 1, what is the algorithm of spectra pre-processing? wavenumber range should be noted in Figure 2 and Figure 3.’ The wavenumber range for the fingerprint region ‘(1800-900 cm-1)’ has been added in brackets in figure captions for Figures 2, 3, and 5. The pre-processing used has been added to all figure captions. ‘Language problems should be considered, and language expression are suggested to be thorough checked and revised by native English speaker.’ The manuscript has been checked by a native English speaker and we believe it meets the high standards expected of a PLOS ONE publication. Journal Requirements Reference list The reference list is complete and correct. Stylisation Level one heading front has been made bold and 18 pt. Level two heading font has been changed to bold and 16 pt. Referral to ‘Figure’ has been shortened to ‘Fig’. ‘Supplementary Figure S1’ has been changed to ‘S1 Fig’. Supporting Information has been listed after the references. The file names have been changed to adhere to the PLOS ONE author guidelines. Author affiliations have been changed to a numerical system. The corresponding author has been designated with an asterisk. Competing Interests We have amended the cover letter to outline that the funding was received from a commercial source and can confirm that this does not alter our adherence to PLOS ONE policies on sharing data and materials. Funding We have amended the cover letter to outline that the funding received from a commercial source and removed mention of funders from the acknowledgement section within the manuscript. Attachments Attachment Submitted filename: Response to Reviewers.pdf https://doi.org/10.1371/journal.pone.0261742.r002
9 Dec 2021 Decision Letter - Du Changwen, Editor Know your enemy: Application of ATR-FTIR spectroscopy to invasive species control PONE-D-21-33488R1 Dear Dr. Holden, 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, Du Changwen Academic Editor PLOS ONE Additional Editor Comments (optional): The revisions are satifactory, and the manuscript is ready for publication. Reviewers' comments: https://doi.org/10.1371/journal.pone.0261742.r003
Formally Accepted
27 Dec 2021 Acceptance Letter - Du Changwen, Editor PONE-D-21-33488R1 Know your enemy: Application of ATR-FTIR spectroscopy to invasive species control Dear Dr. Holden: 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 Professor Du Changwen Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0261742.r004

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