Investigations of the mechanisms of interactions between four non-conventional species with Saccharomyces cerevisiae in oenological conditions

Oliver Harlé; Judith Legrand; Catherine Tesnière; Martine Pradal; Jean-Roch Mouret; Thibault Nidelet

doi:10.1371/journal.pone.0233285

Peer Review History

Original SubmissionNovember 18, 2019
10 Feb 2020 Decision Letter - Yoshikazu Ohya, Editor PONE-D-19-31984 Investigations of the mechanisms of interactions between four non-conventional species with Saccharomyces cerevisiae in oenological conditions. PLOS ONE Dear Dr Nidelet, Thank you for submitting your manuscript to PLOS ONE. First of all, we are sorry that it took long time to review your manuscript. 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. ============================== Especially, the reviewer #1 raised several concerns. Please address these points one by one. ============================== We would appreciate receiving your revised manuscript by Mar 26 2020 11:59PM. 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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 2. PLOS requires an ORCID iD for the corresponding author in Editorial Manager on papers submitted after December 6th, 2016. Please ensure that you have an ORCID iD and that it is validated in Editorial Manager. To do this, go to ‘Update my Information’ (in the upper left-hand corner of the main menu), and click on the Fetch/Validate link next to the ORCID field. This will take you to the ORCID site and allow you to create a new iD or authenticate a pre-existing iD in Editorial Manager. Please see the following video for instructions on linking an ORCID iD to your Editorial Manager account: https://www.youtube.com/watch?v=_xcclfuvtxQ [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: No 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: 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: The authors made the following assumption : « all cultures that produced more than 80g CO2.L-1 (90% of Sc maximum) within 300 hours will be able to complete fermentation » This assumption is not supported by any scientific evidence. The authors should have followed the entire fermentation kinetics in order to interpret the data correctly. In the summary the authors stated : » M. pulcherrima and M. fructicola displayed a negative interaction with the S. cerevisiae strain tested, with a decrease in viability in co-culture, probably due to iron depletion via the production of pulcherriminic acid. The authors suggest iron depletion to be responsible for viability decrease, however, no results presented in this paper support this hypothesis, already reported. Summary is not the place for such assumption. The first part of the discussion is redundant with the result. One of the conclusion is : Meanwhile NS fermentations present similarities, it was possible to group the NS strains performance according to their genus. This is an overinterpretation, taking into account the small number of tested genus and tested strains. The overall discussion is quite poor with very few references to support the comments. For example, regarding the role of lipids that could play a role in the interactions, there is no reference, while some works do exist. CO2 should be written CO2 in legend Reviewer #2: The manuscript is concise and easy to follow. The authors have evaluated the interactions between Saccharomyces cerevisiae and four non-Saccharomyces species with focus on metabolic interactions in particular nutrient resource utilization. A couple of different interaction mechanisms could be identified. One limitation to this study is that only single strains were used for each species, and the authors should at least acknowledge the fact that there might be strain variability and briefly discuss this. Overall, the study set-up is sound but would have benefited from multiple strains per species. Some minor corrections in text are necessary to improve the quality of the paper. These are as follows: Throughout the document, replace “isolated cultures” with either ‘single cultures’ or ‘monocultures’ The use of “strain” in this manuscript is confusing since only single strains were used for each species. Perhaps the authors should rather consider just referring to the species. All the images used for the figures are poor quality and no easy to read through Page 2 line 8: “and” should not be in italics Page 3 line 6: “aiming” should be aimed Page 4 line 75: “smocky” should be smoky Page 5 line 101: “choose” should be chose Page 6 line 135: “corresponds” should be correspond Page 7 line 147: change “on the opposite” to Conversely or In contrast Page 7 line 151: “µm” should be µM Page 8 line 178: insert space between 300 and h Page 8 line 185-186: the part of the sentence starting with “whereas” does not make sense Page 9 line 217: change “isolated” to monoculture Page 9-10 line 217-219: the author indicates no significant difference between mixed cultures and their corresponding mono cultures, but this is not true for the Hu and Mp cultures. Page 11 line 252: “decreasing” is in a different font type from the rest of the text Page 12 line 275: which PCA and Figure 5 is the author referring to? Page 12 line 280: remove “nevertheless” and start the sentence with “Despite” Page 12 line 286 – 290: the authors should refer to studies that have been done on oxygen e.g. Shekhawat et al. 2017 and 2018, Morales et al., 2015 Page 14 line 320: replace “evidence” with observe ****** 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: 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.0233285.r001
Revision 1
31 Mar 2020 Author Response Reviewer #1: The authors made the following assumption : « all cultures that produced more than 80g CO2.L-1 (90% of Sc maximum) within 300 hours will be able to complete fermentation » This assumption is not supported by any scientific evidence. The authors should have followed the entire fermentation kinetics in order to interpret the data correctly. This part was not clearly described, thus the sentence has been completely rewrote to clarify the point and data concerning the maximum level of CO2 produced have been given. See lines 125-130. Moreover, this point has been discussed in the discussion section (see lines 251-264 with reference added). In the summary the authors stated : » M. pulcherrima and M. fructicola displayed a negative interaction with the S. cerevisiae strain tested, with a decrease in viability in co-culture, probably due to iron depletion via the production of pulcherriminic acid. The authors suggest iron depletion to be responsible for viability decrease, however, no results presented in this paper support this hypothesis, already reported. Summary is not the place for such assumption. The sentence “probably due to iron depletion via the production of pulcherriminic acid” has been removed from the abstract (see lines 35-36). The first part of the discussion is redundant with the result. This part has been rewrote to take this remark into account (see lines 244-365 with reference added). One of the conclusion is : Meanwhile NS fermentations present similarities, it was possible to group the NS strains performance according to their genus. This is an overinterpretation, taking into account the small number of tested genus and tested strains. This point has been discussed lines 257-270. The overall discussion is quite poor with very few references to support the comments. Numerous changes have been performed in particular with the addition of new references to support our comments (lines 244-365). For example, regarding the role of lipids that could play a role in the interactions, there is no reference, while some works do exist. References have been added (see paragraph 285-302). CO2 should be written CO2 in legend (done) Reviewer #2: The manuscript is concise and easy to follow. The authors have evaluated the interactions between Saccharomyces cerevisiae and four non-Saccharomyces species with focus on metabolic interactions in particular nutrient resource utilization. A couple of different interaction mechanisms could be identified. One limitation to this study is that only single strains were used for each species, and the authors should at least acknowledge the fact that there might be strain variability and briefly discuss this. Overall, the study set-up is sound but would have benefited from multiple strains per species. Some minor corrections in text are necessary to improve the quality of the paper. These are as follows: Throughout the document, replace “isolated cultures” with either ‘single cultures’ or ‘monocultures’ “Isolated cultures” has been replaced by “Monocultures” lines 94, 161 and throughout the paper. The use of “strain” in this manuscript is confusing since only single strains were used for each species. Perhaps the authors should rather consider just referring to the species. This has been done throughout the paper. All the images used for the figures are poor quality and no easy to read through Page 2 line 8: “and” should not be in italics. (This has been done line 28.) Page 3 line 6: “aiming” should be aimed (done line 64) Page 4 line 75: “smocky” should be smoky (done line 74) Page 5 line 101: “choose” should be chose (done line 100) Page 6 line 135: “corresponds” should be correspond (done line 134) Page 7 line 147: change “on the opposite” to Conversely or In contrast (done lines 147) Page 7 line 151: “µm” should be µM (done line 151) Page 8 line 178: insert space between 300 and h (done line 179) Page 8 line 185-186: the part of the sentence starting with “whereas” does not make sense (sentence changed lines 187-188) Page 9 line 217: change “isolated” to monoculture (done line 210) Page 9-10 line 217-219: the author indicates no significant difference between mixed cultures and their corresponding mono cultures, but this is not true for the Hu and Mp cultures. (This has been clarified lines 218-220) Page 11 line 252: “decreasing” is in a different font type from the rest of the text OK Page 12 line 275: which PCA and Figure 5 is the author referring to? The paragraph has been removed. Page 12 line 280: remove “nevertheless” and start the sentence with “Despite” The paragraph has been removed. Page 12 line 286 – 290: the authors should refer to studies that have been done on oxygen e.g. Shekhawat et al. 2017 and 2018, Morales et al., 2015 (references added line 297) Page 14 line 320: replace “evidence” with observe (OK) Attachments Attachment Submitted filename: renamed_8b108.docx https://doi.org/10.1371/journal.pone.0233285.r002
4 May 2020 Decision Letter - Yoshikazu Ohya, Editor Investigations of the mechanisms of interactions between four non-conventional species with Saccharomyces cerevisiae in oenological conditions. PONE-D-19-31984R1 Dear Dr. Nidelet, 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. 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. Shortly after the formal acceptance letter is sent, an invoice for payment will follow. 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With kind regards, Yoshikazu Ohya, PhD 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 #3: 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 #3: Yes ****** 3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes Reviewer #3: Yes ****** 4. Have the authors made all data underlying the findings in their manuscript fully available? The PLOS Data policy 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: No Reviewer #3: 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 #3: 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: (No Response) Reviewer #3: The authors have adequately addressed reviewer's comments, and the manuscript is now acceptable for publication. ****** 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 #3: No https://doi.org/10.1371/journal.pone.0233285.r003
Formally Accepted
12 May 2020 Acceptance Letter - Yoshikazu Ohya, Editor PONE-D-19-31984R1 Investigations of the mechanisms of interactions between four non-conventional species with Saccharomyces cerevisiae in oenological conditions. Dear Dr. Nidelet: 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. Yoshikazu Ohya Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0233285.r004

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