PONE-D-20-38799

Water and fertilizer managements affect nitrogen and phosphorus losses by surface runoff and microbial communities in a paddy soil

PLOS ONE

Dear Dr. Huang,

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 Feb 18 2021 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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We look forward to receiving your revised manuscript.

Kind regards,

Dayong Zhao, Ph.D.

Academic Editor

PLOS ONE

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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: Partly

Reviewer #2: Partly

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2. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #1: Yes

Reviewer #2: Yes

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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

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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: No

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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: Evaluation of nutrient losses from paddy soils under different irrigation and fertilization practices is important for sustainable management. Authors tried to assess nutrient losses under different water and fertilizer managements and to identify underlying mechanisms. However, the part of results and discussions are not robust. Besides, no significant highlight is established in the present form of manuscript. The present form of this manuscript is not recommended for publication in this journal.

The paper seems technically sound, but I have some doubts regarding the scientific validity and the rigor in science.

(1) Surface runoff should be primarily determined by water depth in the field and the size of rainfall events, rather than soil microorganism composition. In general, a higher water level results in more nutrient losses through surface runoff. Compared with the water depth (1-6 cm) in T1 (traditional irrigation), the water depth (-3-3 cm) in T2 (shallow intermittent irrigation) was relatively lower. Therefore, the risk of nutrient loss under T1 should be higher than it under T2. Hence, the major result of the decline of nutrient losses in T2 is not significant and surprised.

(2) There is a lack of figure, such as SEM, which comprehensively shows the direct effects of various environmental factors on nutrient losses, and its indirect effects through altering microorganism community composition. Besides studied environmental variables (Table 2), the size of rainfall events should be considered in investigating influencing factors of nutrient losses.

Specific comments:

Abstract

(1) The effect of microorganism community composition on nutrient runoff losses should be demonstrated specifically.

(2) More details about T1 and T2 should be given.

Introduction

(1) Line 55-57, the relationship between ammonia oxidation and nitrogen losses should be elaborated.

(2) Line 81, the objective of this study was only to verify an existing irrigation practice. The “develop” is not appropriate.

Materials and methods

(1) Line 107, why did you choose 20 cm as the height of the concrete cement border? I think the quantity of runoff is mainly depended on the height of the border.

(2) Line 109, it’s better to show a figure of the runoff collection device.

Results

(1) Line 211, there are too many significant numbers.

(2) The content of 3.5 part is not closely related to the main purpose of this study. The effects of abiotic factors on the microbial community composition should not be demonstrated in an independent part. The relationship between microorganisms and nutrient losses should be addressed specifically.

Discussion

(1) Line 285-286, please keep constant citation format in the text. Wang et a. (2019) is different from others.

(2) Line 285, the sentence “NO3--N was the main form of TN” doesn’t seem scientific.

(3) Line 313, please delete one “the”.

(4) About 4.3 part, the relationship between microorganisms and environmental factors is not the critical issue in this study. Please rewrite and rename this part.

Tables and Figures

(1) Only fertilization treatment was given in the Table 1. Please add irrigation treatment.

(2) All tables and figures should be improved. The number and letters in the figures are too small.

(3) About Fig. 2 B, Y-axis number “0.000-8.000” should be changed into “0-8”. Please correct other similar issues.

(4) Figure resolution need to be improved.

Reviewer #2: Dear Editor and authors,

PONE-D-20-38799 entitled “Water and fertilizer managements affect nitrogen and phosphorus losses by surface runoff and microbial communities in a paddy soil” have done nice work but being poorly presented. The MS maybe accepted after major revision as followings:

1. The language should be revised deeply through the MS, even in Title, please ask a specialist for help. The title should be “Nitrogen and phosphorus losses by surface runoff and soil microbial communities in a paddy field with different irrigation and fertilization managements”

2. Line 14, please clearly define of T1.

3. Line 28 What is the optimum rice yield?

4. Line 36 the total cultivated area in where?

5. In the introduction parts, the authors should clearly figure out the novelty of your study as there were plenty of literature on N and P losses from paddy fields with different water and fertilization managements.

6. Line 77 This knowledge gap is what? This should be clearly stated.

7. Table 1’ title should be Fertilization schemes for the different treatments. But the authors said that “The water and fertilizer practices used in this experiment are described in Table 1”, where is water managements? On other words, which kind of water-saving irrigation method you used in this study? Please clearly shown your experimental design, which is vital for the readers.

8. 2.2 Water sampling methods should be described in details.

9. Results this parts should be clearly and concise. Line 198 (2795 ± 165 t ha−1) should be deleted as the value has been shown in the Table 2, so many presentation in the results.

10. Why you only shown the relate data obtained from 2018? If you want to make concise, please at least to state this in the Data analysis.

11. Do not simply repeat the results in the Discussion parts.

12. The authors mentioned that “Runoff DN loss was mainly in the form of NO3-–N than in NH4+–N under different water and fertilizer treatments” and given the reasons. I thinks the differences in N and P losses among the different treatments was your mainly focus, and should be deeply discussed.

13. Is there any relationship between soil physiochemical properties and N and P losses? This should be one important novelty of this study.

14. The conclusions should be further clarified.

15. All figures need to be clearly presented, and a lot of texts in figures are not visible.

Best wishes!

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Reviewer #1: No

Reviewer #2: No

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PONE-D-20-38799R1

Nitrogen and phosphorus losses  by surface runoff and soil microbial communities in a paddy field with different irrigation and fertilization managements

PLOS ONE

Dear Dr. Huang,

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.

I appreciate the revisions made. Although two reviewers agreed to accept the article, some additional comments are provided from an editorial standpoint. Most are rather specific and should be easy to address.

Please submit your revised manuscript by Jul 03 2021 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.

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: http://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,

Dayong Zhao, Ph.D.

Academic Editor

PLOS ONE

Journal Requirements:

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.

Additional Editor Comments (if provided):

I appreciate the revisions made. Although two reviewers agreed to accept the article, some additional comments are provided from an editorial standpoint. Most are rather specific and should be easy to address.

Specific comments:

Line 14. Change “Therefore” to “Here or In this study”.

Line 34. Please provide the full name of the abbreviation of N and P, though they have been defined in the abstract section.

Line 36-37. Please cite one reference for this sentence.

Line 37. Please add “,” between “To date” and “water-quality”.

Line 49. Change “For example, Chen et al. (2018) reported that” to “It has been reported that”.

Line 53. Change “For instance,” to “Related studies have suggested that”.

Lien 57-60. Please consider the deletion of these sentences.

Line 64-66. We all know that high-throughput sequencing is widely used in determining the diversity and composition of soil microbes. These sentences did not provide very useful information. Thus, please consider removing the sentences.

Line 67. Remove the “Moreover”.

Line 79-84. According to the title and abstract, different irrigation and fertilization practices could affect soil physicochemical properties and correspondingly influence soil microbial communities, and thereby contribute to N and P runoff losses. Am I right? However, this part has nothing to do with soil microorganisms. Your hypothesis also does not relate to microorganisms.

Line 174-183. What did you do with singleton sequences (i.e., sequence appearing only one time in the entire data set)? Moreover, how do you address uneven sequencing depth across samples? Please be clearer in your presentation.

Line 176-181. Please provide the versions of UPARSE, Silva rRNA database, Mothur software and insert references for them.

Line 179. The authors mentioned that you obtained rarefaction curves using Mothur software, where is the result of rarefaction curves?

Line 193 and Line 200. Both Rstudio and R were used in this study to perform statistical analyses. Please provide their versions in your manuscript and insert reference.

Line 194. Provide the version of the R pheatmap package and cite one reference.

Line 199-200. Which distance did you use? Please make it clear.

Line 197. The “vif” is an abbreviation form. Please define it at its first mention.

Line 200. Provide the version of R vegan package, and then insert one reference for it.

Line 241. Double “the”.

Line 263-267. According to the description of microbial alpha diversity indices in Line 180, change “Ace” to “ACE” and change “Chao” to “Chao1” in the table 4. Meanwhile, provide the explanation of ACE in the table notes in Line 264-267.

Line 306-307. Other environmental factor refer to what? And they would directly affect the N and P losses. I think this sentence can be removed as what is needed in the results section is for the author to describe their findings objectively.

Figures

Figure 1. This image needs to be cropped appropriately as there is a lot of white space throughout the image.

Figure 3. As an example, the font of the words “Runoff yield” and “TN loss loads” in the vertical titles did not seem to correspond to the font of the horizontal title. Please unify the font of all the text in the figure A, B, C and D. In addition, there are up ticks and right ticks in the X-axis and Y-axis of Fig. 3D, respectively, while all ticks in Fig. 3A, 3B and 3C are not shown. Please unify the drawing style. As for Fig. 3D, my suggestion is that the authors can show down ticks and left ticks in X-axis and Y-axis, respectively.

Figure 3B. A point to note in the illustration of the types of line in the image is that the presentation of "NO3--N" and "NH4+-N" should be revised as they are not presented in a very aesthetically pleasing way.

Figure 3D. There are no data points between 0 and 0.6 mg/L of total phosphorus concentration, so the authors could have left the values of the horizontal coordinates not starting from 0.

Figure 4. The word “Venn” and three solid dots with “T0/T1/T2” could be removed from your figure as they are redundant. In addition, the size of the words (e.g., T0, T1 and T2) and numbers in the Venn plots needs to be slightly adjusted upwards. Figure 4A: The bar diagram has two ticks at the value 200 of the vertical coordinate, please deal with them.

Figure 5. Please delete the word “PLS-DA on OTU level” at the top of the figure.

Figure 6. Only major phyla are presented in each treatment. What is the relative abundance of phyla below which they are classified as 'Others'? This needs to be made clear in the figure caption. In addition, please delete the word “Community barplot analysis” at the top of the figure.

Figure 7. Please delete the word “db-RDA on OTU level” at the top of the figure.

Figure 8. Please delete the word “Spearman Correlation Heatmap” at the top of the figure.

Figure 3-Figure 9: The numbers 0, 1 and 2 are below the letter T (i.e., the form of a subscript) in the figure captions and main text. However, in the figure, the author does not show the T0, T1 and T2 in a subscript form, so please standardize the format of presentation.

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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 #2: (No Response)

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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 #2: Yes

**********

3. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #1: Yes

Reviewer #2: 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

Reviewer #2: 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 #2: 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 #2: (No Response)

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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 #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.]

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.

Nitrogen and phosphorus losses by surface runoff and soil microbial communities in a paddy field with different irrigation and fertilization managements

PONE-D-20-38799R2

Dear Dr. Huang,

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.

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Kind regards,

Dayong Zhao, Ph.D.

Academic Editor

PLOS ONE

Additional Editor Comments (optional):

Reviewers' comments: