Fibrolytic rumen bacteria of camel and sheep and their applications in the bioconversion of barley straw to soluble sugars for biofuel production

Alaa Emara Rabee; Amr A. Sayed Alahl; Mebarek Lamara; Suzanne L. Ishaq

doi:10.1371/journal.pone.0262304

Peer Review History

Original SubmissionJuly 27, 2021
12 Nov 2021 Decision Letter - Sabir Hussain, Editor PONE-D-21-24385Fibrolytic rumen bacteria of camel and sheep and their applications in biofuel productionPLOS ONE Dear Dr. Rabee, 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 within 30 days. 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: https://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, Sabir Hussain 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. We note that you are reporting an analysis of a microarray, next-generation sequencing, or deep sequencing data set. PLOS requires that authors comply with field-specific standards for preparation, recording, and deposition of data in repositories appropriate to their field. Please upload these data to a stable, public repository (such as ArrayExpress, Gene Expression Omnibus (GEO), DNA Data Bank of Japan (DDBJ), NCBI GenBank, NCBI Sequence Read Archive, or EMBL Nucleotide Sequence Database (ENA)). In your revised cover letter, please provide the relevant accession numbers that may be used to access these data. For a full list of recommended repositories, see http://journals.plos.org/plosone/s/data-availability#loc-omics or http://journals.plos.org/plosone/s/data-availability#loc-sequencing. 3. Thank you for stating the following in the Acknowledgments Section of your manuscript: This project was supported by the USDA National Institute of Food and Agriculture, Hatch Project Number ME0-022102 through the Maine Agricultural & Forest Experiment Station. Maine Agricultural and Forest Experiment Station Publication Number XXX. We note that you have provided additional information within the Acknowledgements Section that is not currently declared in your Funding Statement. 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: The author(s) received no specific funding for this work. Please include your amended statements within your cover letter; we will change the online submission form on your behalf. 4. 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. 5. Please review your reference list to ensure that it is complete and correct. If you have cited papers that have been retracted, please include the rationale for doing so in the manuscript text, or remove these references and replace them with relevant current references. Any changes to the reference list should be mentioned in the rebuttal letter that accompanies your revised manuscript. If you need to cite a retracted article, indicate the article’s retracted status in the References list and also include a citation and full reference for the retraction notice. [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: I think the research is interesting. However, was there anything novel about the functionality of the rumen microbial community in sheep and camels? was not sufficiently appealing to me. For example, it would be good if the differences between the rumen microbial community of sheep and camels and that of other rumen microbes could be more clearly expressed in graphs. ****** 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.] 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. Attachments Attachment Submitted filename: Comments.docx https://doi.org/10.1371/journal.pone.0262304.r001
Revision 1
29 Nov 2021 Author Response PlOS ONE editorial office Fibrolytic rumen bacteria of camel and sheep and their applications in the bioconversion of barley straw to soluble sugars for biofuel production We thank you and the Reviewers for their constructive comments and corrections. We responded to all comments and have extensively modified many sections in the paper to correct grammatical and style errors. I also enclosed unclean paper including all comments colored by yellow. Below are the responses to all the comments. We made a slight modification in the title of the manuscript. Our paper was improved greatly after the response to the reviewers’ comments. We appreciate the opportunity to submit our manuscript to PlOS ONE. Yours sincerely, Dr. Alaa Rabee Researcher at Desert Research Center, Egypt On behalf of all authors Comments Manuscript title: “Fibrolytic rumen bacteria of camel and sheep and their applications in the bioconversion of barley straw to soluble sugars for biofuel production” In the unclean or marked manuscript you could notice that colored comments using yellow. Responses I think the research is interesting. However, was there anything novel about the functionality of the rumen microbial community in sheep and camels? was not sufficiently appealing to me. For example, it would be good if the differences between the rumen microbial community of sheep and camels and that of other rumen microbes could be more clearly expressed in graphs. >> Thank so much, we added a small comparison at the end of discussion and added supplementary figure that compare the relative abundances of main bacterial groups in our study and in the rumen of other ruminant animals. Figure1 Electron micrographs were not clear, so it is difficult to see the microorganisms attached to the surface of straws. Change to a clearer photo? Or isn't it necessary to include a photo? >>We removed it, unfortunately we don’t have another photos. We had to take photos at different incubation times before 72 h to get clear photos for bacterial colonization. Table1 Please add the unit of gas production. >> Thank you, we added it and scanned all tables for similar mistaks. Table1 "Inoculum Source" means “samples after 72 hours incubation”, is it correct? Please have a representation of what the sample is so that everyone can understand what it was. >> Thank you, inoculum Source refers to animal source of rumen samples that were inoculated into barley straw plus bacterial media, camel or sheep; we clarified that throughout the manuscript. Table 1　What does "overall" in Table 1 mean? I think that DNA extraction is extracting the solid (i.e., attached to the straw), but does "overall" include not only the solid but also the cultured liquid? Is it correct to say that the term "overall" includes not only solids but also cultured liquids? Please describe this in an easy-to-understand manner. >> Thank you for this valuable comment. Overall refers to overall mean of the values in camels and sheep (6 samples: 3 for sheep and 3 for camels), we clarified that in all tables. I did not understand, why you wrote camel rumen sample to “FC”, and inoculum sheep was “FR”. Wouldn't it be better to be consistent all the time in the paper, with camel samples and sheep samples? >> Thank you, we modified that in the text and tables. We stuck with inoculum instead of sample throughout the manuscript, we modified that. Tables 3 please add the units for value. (%). >> We added it and scanned the tables for similar mistakes. Line 435 : This time, the barley straw is autoclaved at 120 degrees Celsius, which I think is quite a heat treatment to the straw. This is a considerable heat treatment. It is possible that the effect of this heat treatment may have increased the hydrolysis efficiency, but what do you think about this? Also, I think this will be a problem when discussing the degradation efficiency when comparing with other papers. So, I think it would be better to have the results of how it was when it was not autoclaved. >>> Thank you for this valuable comment. We used three serum bottles (medium + barley straw) without inoculation as blanks to allow the correction for dry matter disappearance during sterilization. However, I support your view; the microbial hydrolysis efficiency could be increased compared to the results of other studies. Therefore, we modified that section. Attachments Attachment Submitted filename: 000-Response to Reviewers.docx https://doi.org/10.1371/journal.pone.0262304.r002
21 Dec 2021 Decision Letter - Sabir Hussain, Editor Fibrolytic rumen bacteria of camel and sheep and their applications in the bioconversion of barley straw to soluble sugars for biofuel production PONE-D-21-24385R1 Dear Dr. Rabee, 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, Sabir Hussain Academic Editor PLOS ONE Additional Editor Comments (optional): Reviewers' comments: https://doi.org/10.1371/journal.pone.0262304.r003
Formally Accepted
27 Dec 2021 Acceptance Letter - Sabir Hussain, Editor PONE-D-21-24385R1 Fibrolytic rumen bacteria of camel and sheep and their applications in the bioconversion of barley straw to soluble sugars for biofuel production Dear Dr. Rabee: 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. Sabir Hussain Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0262304.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 .