Peer Review History
| Original SubmissionJuly 21, 2019 |
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PONE-D-19-20527 Divulging diazotrophic bacterial community structure in Kuwait desert ecosystems and their N2-fixation potential PLOS ONE Dear Dr. Quoreshi, 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. We would appreciate receiving your revised manuscript by Nov 09 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:
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, Andrew R. Zimmerman, PhD Academic Editor PLOS ONE Journal Requirements: When submitting your revision, we need you to address these additional requirements. 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 1. 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. 2. We suggest you thoroughly copyedit your manuscript for language usage, spelling, and grammar. If you do not know anyone who can help you do this, you may wish to consider employing a professional scientific editing service. Whilst you may use any professional scientific editing service of your choice, PLOS has partnered with both American Journal Experts (AJE) and Editage to provide discounted services to PLOS authors. Both organizations have experience helping authors meet PLOS guidelines and can provide language editing, translation, manuscript formatting, and figure formatting to ensure your manuscript meets our submission guidelines. To take advantage of our partnership with AJE, visit the AJE website (http://learn.aje.com/plos/) for a 15% discount off AJE services. To take advantage of our partnership with Editage, visit the Editage website (www.editage.com) and enter referral code PLOSEDIT for a 15% discount off Editage services. If the PLOS editorial team finds any language issues in text that either AJE or Editage has edited, the service provider will re-edit the text for free. Upon resubmission, please provide the following:
3. We note that you have included the phrase “data not shown” in your manuscript. Unfortunately, this does not meet our data sharing requirements. PLOS does not permit references to inaccessible data. We require that authors provide all relevant data within the paper, Supporting Information files, or in an acceptable, public repository. Please add a citation to support this phrase or upload the data that corresponds with these findings to a stable repository (such as Figshare or Dryad) and provide and URLs, DOIs, or accession numbers that may be used to access these data. Or, if the data are not a core part of the research being presented in your study, we ask that you remove the phrase that refers to these data. Additional Editor Comments (if provided): The manuscript is suitable for publication but needs some minor adjustments. please make the changes indicated by the 2 external reviewers. In addition, I ask that you try to have the text edited by a native English speaker as there are many grammatical errors. In addition, a reviewer commented that "more logical explanations which would definitely enhance the quality of this manuscript". Thus, I ask that you go through the Discussion section, making sure the argument flows logically. Perhaps add some subheadings to indicate topics being discussed and divide some of the longer paragraphs into a few shorter ones. [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 Reviewer #2: Yes ********** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes Reviewer #2: N/A ********** 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: No 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: Yes 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: 1. At line no. 27 you have used BNF as abbreviation for Biological nitrogen fixation. However, at line no 74 you are using same abbreviation for Biological nitrogen fixers. Please correct this, both biological nitrogen fixation and biological nitrogen fixers are absolutely different. 2. At line no 116, please explain the methodology of rhizospheric soil sample collection in details. 3. Please put space between number and °C throughout the manuscript. For example write 10 °C instead of 10°C. 4. Please make the tables compact. It would be easy to understand data if more information is present in single page rather than the multiple pages. 5. In line no 434 please replace N2 with N2. 6. At line no 461 the authors have written “In this investigation, a structure resembles to root nodule often found in Leguminaceae plant roots was observed and assumed similar to typical nitrogen-fixing root nodules produced by Rhizobium sp.”. How could you make this statement without showing results of nodule characterization? Please justify the about statement written in the manuscript. 7. Image quality of figures is very poor. Please incorporate high quality images. 8. This study is showing that Agrobacterium tumefaciens, which has been renamed as Rhizobium radiobacter, was recovered by root nodules and have potential to fix atmospheric nitrogen outside of the host as shown in ARA based analysis. However, other nodules forming Rhizobium species does not fix nitrogen outside of the host. Moreover, characterization of the bacterial isolates is only based on the partial 16S rDNA sequencing which do not have sufficient resolution to characterize closely related bacterial species. Therefore, please explain your results more clearly and logically. Please go through the following article as it can help you to explain your results in more details: Velázquez, E., Peix, A., Zurdo-Piñiro, J. L., Palomo, J. L., Mateos, P. F., Rivas, R., ... & Martínez-Molina, E. (2005). The coexistence of symbiosis and pathogenicity-determining genes in Rhizobium rhizogenes strains enables them to induce nodules and tumors or hairy roots in plants. Molecular plant-microbe interactions, 18(12), 1325-1332. Reviewer #2: The authors enriched and isolated several number of free and symbiotic N2-fixers from rhizosphere and root nodes of four plant species in Kuwait semi-arid desert ecosystem. Apart from precipitation, nitrogen is important for plant growth and microbial nitrogen-fixers play essential roles in nitrogen supply for the semi-arid desert ecosystem. The isolation of many nitrogen-fixing bacteria can pave the way to fully understand N cycling in the special ecosystem, and it shows the most significance especially in the modern popular "metagenomics" era. The manuscript has been well organized and the materials and methods were well described. There was only minor parts needed to be revised: Discuss the differences in microbial compositions between this study and other studies/ ecosystems. L34-36, repetead sentences "In this study,......species" L84, precipitation is also important L375, references? L376, Are there any differences in microbial compositions between this study and other studies/ ecosystems? What's the difference? ********** 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. |
| Revision 1 |
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PONE-D-19-20527R1 Divulging diazotrophic bacterial community structure in Kuwait desert ecosystems and their N2-fixation potential PLOS ONE Dear Dr. Quoreshi, 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. We would appreciate receiving your revised manuscript by Dec 15 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:
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, Andrew R. Zimmerman, PhD Academic Editor PLOS ONE Additional Editor Comments (if provided): Dear Suleiman, I have just a few more requests of you. First, I have further edited your abstract as I feel this is really important to get right. See if you agree with my suggestions: (Track change version in the attached) Kuwait is a semi-arid region with soils that are relatively nitrogen-poor. Thus, biological nitrogen fixation is an important natural process in which N2-fixing bacteria (diazotrophs) convert atmospheric nitrogen into plant-usable forms such as ammonium and nitrate. Currently, there is limited information on free-living and root-associated nitrogen-fixing bacteria and their potential to fix nitrogen and aid natural plant communities in the Kuwait desert. In this study, free living N2-fixing diazotrophs were enriched and isolated from the rhizosphere soil associated with three native keystone plant species; Rhanterium epapposum, Farsetia aegyptia, and Haloxylon salicornicum. Root-associated bacteria were isolated from the root nodules of Vachellia pachyceras. The result showed that the strains were clustered in five groups including the Actinobacteria being the most dominant phyla followed by Firmicutes, and the classes β-proteobacteria γ-proteobacteria, and α-proteobacteriaThis study initially identified 50 nitrogen-fixers by16S rRNA gene sequencing, of which 78% were confirmed to be nitrogen-fixers using the acetylene reduction assay. Among the nitrogen fixers identified, the genus Rhizobium was predominant in the rhizosphere soil of R. epapposum and H. salicornicum, whereas Pseudomonas was predominant in the rhizosphere soil of F. aegyptia, . The species Agrobacterium tumefaciens was dominant in the root nodules of V. pachyceras. These results indicate that plant species and their rhizosphere effects are important drivers of diazotroph diversity in arid soils. To our knowledge, this study is the first to use culture-based isolation, molecular identification, and evaluation of N2-fixing ability to detail diazotroph diversity in Kuwaiti desert soils. Second, I would like you to put a bit more thought into your conclusion section. The statement "most species belonged to the Rhizobium, Pseudomonas, and Agrobacterium genera followed by Cellulomonas, and Bacillus genera" seems quite different from what you have in the abstract. Or maybe I misunderstand and this information should go into the abstract. But beyond that, the abstract should not just restate the results. I would rather like to see it include a statement of the broader ecological/scientific significance of the results. [Note: HTML markup is below. Please do not edit.] [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.
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| Revision 2 |
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Divulging diazotrophic bacterial community structure in Kuwait desert ecosystems and their N2-fixation potential PONE-D-19-20527R2 Dear Dr. Quoreshi, 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. 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, Andrew R. Zimmerman, PhD Academic Editor PLOS ONE Additional Editor Comments (optional): Reviewers' comments: |
| Formally Accepted |
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PONE-D-19-20527R2 Divulging diazotrophic bacterial community structure in Kuwait desert ecosystems and their N2-fixation potential Dear Dr. Quoreshi: 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. Andrew R. Zimmerman Academic Editor PLOS ONE |
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