Genome analysis of biosurfactant producing bacterium, Bacillus tequilensis

Anuraj Nayarisseri; Sanjeev Kumar Singh

doi:10.1371/journal.pone.0285994

Peer Review History

Original SubmissionJuly 9, 2022
5 Jan 2023 Decision Letter - Pankaj Kumar Arora, Editor PONE-D-22-19370Whole-Genome Sequencing and Annotation of Biosurfactant Producing Bacillus tequilensisPLOS ONE Dear Dr. Singh, 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 26 2023 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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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. In your Methods section, please provide additional information regarding the permits you obtained for the work. Please ensure you have included the full name of the authority that approved the field site access and, if no permits were required, a brief statement explaining why. 3. 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): 1. Title should be changed as "Genome analysis of biosurfactant producing bacterium, Bacillus tequilensis. 2. All microorganisms name should be italics. 3. Data related to genome-based taxonomy including average nucleotide identity and digital DNA-DNA hybridization with closely related type strains should be provided. 4. These lines are incorrect "we concluded that Bacillus tequilensis produces biosurfactants and the novel isolate was deposited in GenBank with accession number KU529483". You have submitted nucleotide sequence of 16S rRNA gene to the Genbank not bacteria. Similar mistakes are in whole manuscript. 5. Manuscript is too lengthy; it should be concise. It should be focused only on biosurfactant related genes. 6. Experimental data related to biosurfactant production in this strain are necessary. [Note: HTML markup is below. Please do not edit.] Reviewers' comments: [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.0285994.r001
Revision 1
24 Feb 2023 Author Response RESPONSE LETTER Ref.: Whole Genome Sequencing and Annotation of Biosurfactant Producing Bacillus tequilensis Dear Editors, We appreciated the review of our manuscript and the suggestions given to make it suitable to PLOS One journal which is in high quality standards. As requested, this letter responds to each point raised by the reviewers. Please, kindly note that changes were marked up in the manuscript and are transcribed herein: Editor Comments 1. Title should be changed as "Genome analysis of biosurfactant producing bacterium, Bacillus tequilensis. Response: We appreciate the careful evaluation of our manuscript and the recommendations made to raise the quality of it. As advised by the editor, we would like to let the editor know that the title of the manuscript has been changed to "Genome study of biosurfactant generating bacteria, Bacillus tequilensis." Thanks. 2. All microorganisms name should be italics. Response: We value the in-depth analysis of our manuscript and the recommendations made for enhancing its quality. We would want to let the editor know that all of the microbe names have been changed to italics as per the editor's suggestion. Thanks. 3. Data related to genome-based taxonomy including average nucleotide identity and digital DNA-DNA hybridization with closely related type strains should be provided. Response: We value the thorough analysis of our manuscript and the suggestions offered to improve its quality. We would like to inform the editor that in section 2.1 first paragraph, we have added the genome-based taxonomy including ANI (Average Nucleotide Identity) analysis and digital DNA-DNA hybridization/ Genome – Genome comparison by GGDC(Genome Genome Distance Calculator) with closely related type strains of Bacillus tequilensis as suggested by the editor. Thanks. 4. These lines are incorrect "we concluded that Bacillus tequilensis produces biosurfactants and the novel isolate was deposited in GenBank with accession number KU529483". You have submitted nucleotide sequence of 16S rRNA gene to the Genbank not bacteria. Similar mistakes are in whole manuscript. Response: We value the thorough analysis of our manuscript and the suggestions offered to improve its quality. We would want to inform the editor that we have changed this throughout the manuscript as suggested by the editor. I appreciate you pointing out this error. 5. Manuscript is too lengthy; it should be concise. It should be focused only on biosurfactant related genes. Response : We appreciate the in-depth evaluation of our manuscript and the recommendations made to raise its quality. Since the work involves a whole genome analysis and complete annotation of a bacteria, we would want to let the editor know that we made every effort to keep the paper as concise as possible. As a result, the text became a little lengthy. We made an effort to discard a few information, such SSR identification. Let us know if there are any other analysis need to be deleted. Looking forward to hear for the suggesion. 6. Experimental data related to biosurfactant production in this strain are necessary. Response : We value the thorough analysis of our manuscript and the suggestions offered to improve its quality. We would like to inform the editor that, we have carried out a number of experimental studies including the Haemolysis test, oil spreading test, CTAB agar plate test, Drop collapse test etc from which we have concluded that the Bacillus tequilensis isolate used in this investigation produces biosurfactants. This study has already been published, so we've used it as a source in result session 2.2 in the present manuscript.The present study is a continuation of the earlier investigation.The publication can be access from the folowign link. https://link.springer.com/article/10.1007/s13762-018-2089-9 Attachments Attachment Submitted filename: Response to Reviewers.docx https://doi.org/10.1371/journal.pone.0285994.r002
7 May 2023 Decision Letter - Pankaj Kumar Arora, Editor Genome analysis of biosurfactant producing bacterium, Bacillus tequilensis PONE-D-22-19370R1 Dear Dr. Singh, 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, Pankaj Kumar Arora 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 ******** 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 ****** 3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: 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 ****** 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 ****** 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: All comments and queries were addressed appropriately. The manuscript can be accepted in the present form. ****** 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 ******** https://doi.org/10.1371/journal.pone.0285994.r003
Formally Accepted
22 May 2023 Acceptance Letter - Pankaj Kumar Arora, Editor PONE-D-22-19370R1 Genome analysis of biosurfactant producing bacterium, Bacillus tequilensis. Dear Dr. Singh: 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. Pankaj Kumar Arora Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0285994.r004

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