Morphological and molecular identification of the dioecious “African species Volvox rousseletii (Chlorophyceae) in the water column of a Japanese lake based on field-collected and cultured materials

Ryosuke Kimbara; Nanako Isaka; Ryo Matsuzaki; Hiroko Kawai-Toyooka; Masanobu Kawachi; Hisayoshi Nozaki

doi:10.1371/journal.pone.0221632

Peer Review History

Original SubmissionJune 22, 2019
16 Jul 2019 Decision Letter - James G. Umen, Editor PONE-D-19-17716 Morphological and Molecular Identification of the Dioecious “African Species” Volvox rousseletii (Chlorophyceae) in the Water Column of a Japanese Lake Based on Field-collected and Cultured Materials PLOS ONE Dear Dr. Nozaki, 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. I agree with Reviewer 1 about the high quality and overall suitability of this manuscript for publication. In your revision and rebuttal please respond to the critiques of Reviewer 1 with whom I also agree regarding the last section where the discussion of Spirogyra and Chloromonas seemed out of place, and the need for details of the KOD polymerase method to be elaborated in the Methods section. One more minor point. In Fig. 1B there are asterisk symbols which are not mentioned in the legend. We would appreciate receiving your revised manuscript by Aug 30 2019 11:59PM. When you are 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. If you would like to make changes to your financial disclosure, please include your updated statement in your cover letter. To enhance the reproducibility of your results, we recommend that if applicable you deposit your laboratory protocols in protocols.io, where a protocol can be assigned its own identifier (DOI) such that it can be cited independently in the future. For instructions see: http://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols 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). This letter should be uploaded as separate file and labeled 'Response to Reviewers'. A marked-up copy of your manuscript that highlights changes made to the original version. This file should be uploaded as separate file and labeled 'Revised Manuscript with Track Changes'. An unmarked version of your revised paper without tracked changes. This file should be uploaded as separate file and labeled 'Manuscript'. 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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. 3. Thank you for stating the following in the Acknowledgments Section of your manuscript: "Funding: HN was supported by a Grant-in-Aid for Scientific Research (grant number 16H02518) from the Ministry of Education, Culture, Sports, Science and Technology (MEXT)/Japan Society for the Promotion of Science (JSPS) KAKENHI (https://www.jsps.go.jp/english/e-grants/). 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 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: "The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript." 4. 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. Additional Editor Comments (if provided): [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: This manuscript details the occurrence of Volvox rousseletii in Japan, the first time this species has been recorded outside of Africa. The manuscript is well written and is both concise and clear. The data presented is micrographs of laboratory cultivated asexual colonies, field collected sexual colonies, and phylogenetic analyses deriving from both asexual and sexual colonies (confirming that the sexual colonies do indeed correspond to the associated asexual strains). Overall the analyses are appropriate, the data recording is meticulous, the micrographs are excellent, and the paper should be published. I have one major comment which should be addressed before publication. While the manuscript title, Abstract, and Introduction emphasizes the characterization of a species thought to be restricted to Africa, the Conclusions section instead emphasizes the challenge of characterizing sexual isolates in culture in Spirogyra and Chloromonas, other algae not previously mentioned. The Conclusions should be revised to address the novelty of this paper, the isolation of V. rousseletii in Japan as emphasized by the title, Abstract, and Introduction. The revised species range for V. rousseletii and availability of fresh cultures is worthwhile and should be emphasized. Similarly, the usage of KOD polymerase, an important methodological detail, should be moved to the Methods. A few minor comments: 1. Hanschen et al 2018 Evol Eco Res published the psbC and rbcL sequences of Volvox perglobator (accession numbers KY489659 and KY489662), these should be included in Figure 5. 2. Page 5, last paragraph “Volvox” should be italicized when introducing VTAC media 3. The implementation of maximum parsimony for phylogenetic analyses is outdated and should be replaced by Bayesian analyses. This analysis can be implemented in MrBayes. 4. Page 9, please do not abbreviate CBCs. 5. Figure 1, the () and (b) are not specified in the legend for panels B and C. ******* 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 [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 to be viewed.] 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 us at figures@plos.org. Please note that Supporting Information files do not need this step. https://doi.org/10.1371/journal.pone.0221632.r001
Revision 1
31 Jul 2019 Author Response PONE-D-19-17716 Morphological and Molecular Identification of the Dioecious “African Species” Volvox rousseletii (Chlorophyceae) in the Water Column of a Japanese Lake Based on Field-collected and Cultured Materials PLOS ONE Dear Dr. Nozaki, 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. I agree with Reviewer 1 about the high quality and overall suitability of this manuscript for publication. In your revision and rebuttal please respond to the critiques of Reviewer 1 with whom I also agree regarding the last section where the discussion of Spirogyra and Chloromonas seemed out of place, and the need for details of the KOD polymerase method to be elaborated in the Methods section. Responses: Based on the comments, the conclusion section has been drastically revised by deleting the discussion of Spirogyra and Chloromonas. Detailed methods of PCR with KOD polymerase have been described in Materials and Methods section of the revised manuscript. One more minor point. In Fig. 1B there are asterisk symbols which are not mentioned in the legend. Response: The asterisk symbols have been specified in the legend for Fig. 1B in the revised manuscript. We would appreciate receiving your revised manuscript by Aug 30 2019 11:59PM. When you are 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. If you would like to make changes to your financial disclosure, please include your updated statement in your cover letter. To enhance the reproducibility of your results, we recommend that if applicable you deposit your laboratory protocols in protocols.io, where a protocol can be assigned its own identifier (DOI) such that it can be cited independently in the future. For instructions see: http://journals.plos.org/plosone/s/submission-guidelines#loc-laboratory-protocols 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). This letter should be uploaded as separate file and labeled 'Response to Reviewers'. • A marked-up copy of your manuscript that highlights changes made to the original version. This file should be uploaded as separate file and labeled 'Revised Manuscript with Track Changes'. • An unmarked version of your revised paper without tracked changes. This file should be uploaded as separate file and labeled 'Manuscript'. Please note while forming your response, if your article is accepted, you may have the opportunity to make the peer review history publicly available. The record will include editor decision letters (with reviews) and your responses to reviewer comments. If eligible, we will contact you to opt in or out. We look forward to receiving your revised manuscript. Kind regards, James G. Umen, 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 http://www.journals.plos.org/plosone/s/file?id=wjVg/PLOSOne_formatting_sample_main_body.pdf and http://www.journals.plos.org/plosone/s/file?id=ba62/PLOSOne_formatting_sample_title_authors_affiliations.pdf Response: We have ensured that our revised manuscript meets PLOS ONE's style requirements 2. 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. 3. Thank you for stating the following in the Acknowledgments Section of your manuscript: "Funding: HN was supported by a Grant-in-Aid for Scientific Research (grant number 16H02518) from the Ministry of Education, Culture, Sports, Science and Technology (MEXT)/Japan Society for the Promotion of Science (JSPS) KAKENHI (https://www.jsps.go.jp/english/e-grants/). 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 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: "The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript." Responses: I have removed any funding-related text from the revised manuscript. We would not like to update our Funding Statement "The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript." 4. 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. Responses: I have included captions for our Supporting Information files at the end of our revised manuscript and updated any in-text citations to match accordingly. I have seen your Supporting Information guidelines Additional Editor Comments (if provided): [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: This manuscript details the occurrence of Volvox rousseletii in Japan, the first time this species has been recorded outside of Africa. The manuscript is well written and is both concise and clear. The data presented is micrographs of laboratory cultivated asexual colonies, field collected sexual colonies, and phylogenetic analyses deriving from both asexual and sexual colonies (confirming that the sexual colonies do indeed correspond to the associated asexual strains). Overall the analyses are appropriate, the data recording is meticulous, the micrographs are excellent, and the paper should be published. I have one major comment which should be addressed before publication. While the manuscript title, Abstract, and Introduction emphasizes the characterization of a species thought to be restricted to Africa, the Conclusions section instead emphasizes the challenge of characterizing sexual isolates in culture in Spirogyra and Chloromonas, other algae not previously mentioned. The Conclusions should be revised to address the novelty of this paper, the isolation of V. rousseletii in Japan as emphasized by the title, Abstract, and Introduction. The revised species range for V. rousseletii and availability of fresh cultures is worthwhile and should be emphasized. Similarly, the usage of KOD polymerase, an important methodological detail, should be moved to the Methods. Responses: Based on the comments, the conclusion section has been drastically revised by deleting the discussion of the challenge of characterizing sexual isolates in culture in Spirogyra and Chloromonas. Revised species range for V. rousseletii and availability of fresh cultures from Japan have been discussed in the conclusion section of the revised manuscript. Detailed methods of PCR with KOD polymerase have been described in Materials and Methods section of the revised manuscript. A few minor comments: 1. Hanschen et al 2018 Evol Eco Res published the psbC and rbcL sequences of Volvox perglobator (accession numbers KY489659 and KY489662), these should be included in Figure 5. Responses: Based on the comment, the psbC and rbcL sequences Volvox perglobator (accession numbers KY489659 and KY489662) have been included in Figure 5 of the revised manuscript. 2. Page 5, last paragraph “Volvox” should be italicized when introducing VTAC media Response: Done as suggested. 3. The implementation of maximum parsimony for phylogenetic analyses is outdated and should be replaced by Bayesian analyses. This analysis can be implemented in MrBayes. Response: The maximum parsimony has been replaced by Bayesian analyses using MrBayes in Figures 4 and 5 of the revised manuscript. 4. Page 9, please do not abbreviate CBCs. Response: Done as suggested. 5. Figure 1, the () and (b) are not specified in the legend for panels B and C. Response: The () and (b) have been specified in the legend for panels B and C in the revised manuscript. Attachments Attachment Submitted filename: Response to Reviewers.docx https://doi.org/10.1371/journal.pone.0221632.r002
13 Aug 2019 Decision Letter - James G. Umen, Editor Morphological and Molecular Identification of the Dioecious “African Species” Volvox rousseletii (Chlorophyceae) in the Water Column of a Japanese Lake Based on Field-collected and Cultured Materials PONE-D-19-17716R1 Dear Dr. Nozaki, We are pleased to inform you that your manuscript has been judged scientifically suitable for publication and will be formally accepted for publication once it complies with all outstanding technical requirements. Congratulations on adding an interesting new set of isolates to the Volvox family. Within one week, you will receive an e-mail containing information on the amendments required prior to publication. When all required modifications have been addressed, you will receive a formal acceptance letter and your manuscript will proceed to our production department and be scheduled for publication. Note that the revised manuscript file set did not include Table S1 which I assume did not change from the first submission. Please remember to send this file to the PLoS ONE editorial staff. Shortly after the formal acceptance letter is sent, an invoice for payment will follow. To ensure an efficient production and billing process, please log into Editorial Manager at https://www.editorialmanager.com/pone/, click the "Update My Information" link at the top of the page, and update your user information. 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 enable them to help maximize its impact. If they will be preparing press materials for this manuscript, you must inform our press team as soon as possible and 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. With kind regards, James G. Umen, Ph. D. Academic Editor PLOS ONE Additional Editor Comments (optional): Reviewers' comments: https://doi.org/10.1371/journal.pone.0221632.r003
Formally Accepted
22 Aug 2019 Acceptance Letter - James G. Umen, Editor PONE-D-19-17716R1 Morphological and Molecular Identification of the Dioecious “African Species” Volvox rousseletii (Chlorophyceae) in the Water Column of a Japanese Lake Based on Field-collected and Cultured Materials Dear Dr. Nozaki: I am 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 notify them about your upcoming paper at this point, to enable them to help maximize its impact. If they will be preparing press materials for this manuscript, 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. For any other questions or concerns, please email plosone@plos.org. Thank you for submitting your work to PLOS ONE. With kind regards, PLOS ONE Editorial Office Staff on behalf of Dr. James G. Umen Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0221632.r004

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