Soil microbial community responses to short-term nitrogen addition in China’s Horqin Sandy Land

Niu Yayi; Duan Yulong; Li Yuqiang; Wang Xuyang; Chen Yun; Wang Lilong

doi:10.1371/journal.pone.0242643

Peer Review History

Original SubmissionNovember 5, 2020
12 Jan 2021 Decision Letter - Tanvir Shahzad, Editor PONE-D-20-34907 Soil microbial community responses to short-term nitrogen addition in China’s Horqin Sandy Land PLOS ONE Dear Dr. Yulong Duan, 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. The reviewer is particularly keen about the overall rationale of the study. For instance, why did the authors choose two closely situated field sites for exploring this research question. Furthermore, there are some results that have not been adequately discussed (see below the comments by the reviewer). Please submit your revised manuscript by February 1, 2021. 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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: The manuscript ‘Soil microbial community responses to short-term nitrogen addition in China’s Horqin Sandy Land (PONE-D-20-34907)’ has been reviewed. The study investigated the effect of short-term N addition on various soil microflora characteristics at three N addition levels in the sandy grassland and semi-fixed sandy land. Overall, idea of the work is good however there are few key questions to be addressed before getting the manuscript suitable for publication in PLOS ONE. The comments are as under. Authors need to build the rational differentiating the variable response of microbial communities upon short term and long-term nitrogen addition – it wasn’t accordingly discussed. Key words should be precise and most relevant, for example site or region presence in key words may not be important. Line 44 cut ‘they’. Authors have mentioned about the response of microbes across forest and farmland as previously reported, assumption behind studying the short-term N addition in sandy grassland and semi-fixed sandy land ecosystems is to be mentioned. The activity of β- 1,4-glucosidasewas increased upon nitrogen addition (N5, N10), could this only be related to the release of nitrogen from plant litter degradation. Why these two particular sites with distance of 1.5 km were chosen when the pedoclimatic condition relying on were (supposedly) the same. For fungal amplification, 18S rRNA could be targeted? Did authors check for inhibition test to remove the background noise before running the qPCR assays? The bacterial gene abundances quantified through 16S RNA gene copy numbers in the sandy grassland and semi-fixed sandy showed a high variation but were there no significant differences. The microbial community structure through targeting ITS region could be a possible way to know the differences in community structure across variable soils as discussed in taxonomic composition. Community composition analyses in nicely described but dominant phyla may be described in result section. The conclusions should not be repetition of results rather focus the key findings. Sincerely, ****** 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: Reviewer Comments_PONE-D-20-34907.pdf https://doi.org/10.1371/journal.pone.0242643.r001
Revision 1
11 Mar 2021 Author Response 25 January 2021 Reviewer PLOS ONE RE: Submission of the revised manuscript (No. PONE-D-20-34907): Soil microbial community responses to short-term nitrogen addition in China’s Horqin Sandy Land. Dear Reviewer: Thank you very much for your assistance in the review of our manuscript. We have revised the manuscript carefully according to your comments. Our detailed responses to comments are presented in the remainder of this letter. All of revisions have been highlighted in red in the revision. 1. Authors need to build the rational differentiating the variable response of microbial communities upon short term and long-term nitrogen addition – it wasn’t accordingly discussed. Thank you for your advice. We have added the discussion about the variable response of microbial communities upon short-term and long-term nitrogen addition (lines 80-90 in the revision). 2. Key words should be precise and most relevant, for example site or region presence in key words may not be important. We agree with your point of view that key words should be precise and most relevant. Follow your comments, we have deleted the site presence and added the soil microbial communities (line 33 in the revision). 3. Authors have mentioned about the response of microbes across forest and farmland as previously reported, assumption behind studying the short-term N addition in sandy grassland and semi-fixed sandy land ecosystems is to be mentioned. Based on your comment, we have added the assumption in the revision (lines 95-98 in the revision). 4. The activity of β- 1,4-glucosidase was increased upon nitrogen addition (N5, N10), could this only be related to the release of nitrogen from plant litter degradation. The activity of β- 1,4-glucosidase mainly releases glucose from cellulose and plays an important role in C cycling (lines 72-74 in the revision).The reason for the activity of β- 1,4-glucosidase was increased upon nitrogen addition (N5, N10) has shown in revision (lines 469-472 in the revision). 5. Why these two particular sites with distance of 1.5 km were chosen when the pedoclimatic condition relying on were (supposedly) the same. The region’s sandy grassland grows on aeolian sandy soils or areas with sandy soils as the substrate and is typical of the grassland vegetation that develops in sandy land (Munkhdalai et al., 2007), the vegetation coverage is about 60%. The dominant plant species were annual herbs, including Artemisia scoparia, Setaria viridis, Salsola collina, and Corispermum hyssopifolium. Semi-fixed sandy land refers to the dune or sandy land where the vegetation coverage is between 10% and 29% and the distribution is uniform, and the movement of wind-sand flow is blocked, but the texture of quicksand still exists widely, the dominant plant species were perennial shrubs Caragana microphylla and annual herbs. Therefore, we tried to explore the response of soil microorganisms in different habitat types to N addition under the process of desertification restoration. Munkhdalai, Z. A., Feng, Z. W., Wang, X. K., and Sun, H. W.: Sandy grassland blowouts in Hulunbuir, northeast China: geomorphology, distribution, and causes, Prog. Nat. Sci.-Mater., 17, 68–73, https://doi.org/10.1080/10020070612331343227, 2007. 6. For fungal amplification, 18S rRNA could be targeted? Yes, 18S rRNA could be targeted for fungal amplification, meanwhile, 18S primers also detected the Vertebrata, Ciliophora, Arthropoda and Bicosoecida (Duan et al., 2018). In this study, we only focused on fungi amplification, therefore, we used ITS rRNA for fungal amplification in our research. Duan, Y. L., Wu, F. S., Wang, W. F., Gu, J. D., Li, Y. F., Feng, H. Y., Chen, T., Liu, G. X., An, L. Z., 2018. Differences of microbial community on the wall paintings preserved in situ and ex situ of the Tiantishan Grottoes, China. Int. Biodeterior. Biodegrad. 7. Did authors check for inhibition test to remove the background noise before running the qPCR assays? Yes, we have checked for inhibition test to make sure the accuracy of qPCR data (lines 204 in the revision). 8. The bacterial gene abundances quantified through 16S RNA gene copy numbers in the sandy grassland and semi-fixed sandy showed a high variation but were there no significant differences. The microbial community structure through targeting ITS region could be a possible way to know the differences in community structure across variable soils as discussed in taxonomic composition. Thank you for your advice. This comment is great helpful to our future research. However, the bacterial gene abundances and the fungal gene abundances were quantified through 16S RNA and ITS rRNA, respectively. The result showed that the bacterial gene abundances and the fungal abundances in the sandy grassland and semi-fixed sandy were no significant differences (lines 507-508 in the revision). Therefore, ITS rRNA may not be as a possible way to explore the differences in community structure in present study. 9. Community composition analyses in nicely described but dominant phyla may be described in result section. We have added the dominant phyla of the bacterial operational taxonomic units (OTUs) and fungal communities and highlighted in red (lines 342-345, 347, 352, 364-367 in the revision). 10. Figures could not be accessed as these were missing in the manuscript file so editor may verify the figures quality. I evaluated the work based on the detail of the manuscript provided. We separately uploaded all the figures during the manuscript submission process, if these figures did not meet the requirements, we can re-upload all the figures to make them accessible. 11. The conclusions should not be repetition of results rather focus the key findings. We have revised the description according to your comments (Line 542-553). Thanks for your efforts to improve our manuscript. We hope that our replies and the resulting changes will be satisfactory, but we will be happy to work with you to resolve any remaining issues. Sincerely, Yulong Duan, Ph.D Northwest Institute of Eco-Environment and Resources Chinese Academy of Sciences 320 Donggang West Road, Lanzhou, 730000, China Phone/Fax: 86-931-496-7219 E-mail: duanyulong@nieer.ac.cn Attachments Attachment Submitted filename: Response to Reviewers.docx https://doi.org/10.1371/journal.pone.0242643.r002
15 Apr 2021 Decision Letter - Tanvir Shahzad, Editor Soil microbial community responses to short-term nitrogen addition in China’s Horqin Sandy Land PONE-D-20-34907R1 Dear Dr. Yulong Duan, 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, Tanvir Shahzad 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: The revised version of the manuscript ‘Soil microbial community responses to short-term nitrogen addition in China’s Horqin Sandy Land (PONE-D-20-34907R1)’ has been reviewed. Dear Editor, Authors have now revised the manuscript in light of comments. Thanks to authors for taking into account my previous comments and recommendations. Currently, the article is sufficiently improved, and is in suitable form for publication in PLOS ONE. However, figures could not be accessed as these were missing in the manuscript file so editor may verify the figures quality. I evaluated the work based on the detail of the manuscript provided. ****** 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.0242643.r003
Formally Accepted
11 May 2021 Acceptance Letter - Tanvir Shahzad, Editor PONE-D-20-34907R1 Soil microbial community responses to short-term nitrogen addition in China’s Horqin Sandy Land Dear Dr. Yulong: 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. Tanvir Shahzad Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0242643.r004

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