PONE-D-21-13677Dynamical conversion of photosynthetic bacterial communities in tomato, cucumber, and soybean fields over different growth periods characterized by high-throughput sequencingPLOS 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: Yes

Reviewer #2: Yes

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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: 1. Summary: Photosynthetic bacteria are an important component of the phyllosphere, as they play roles in plant health, plant function, and disease suppression. Though there are potential applications for agricultural production, many photosynthetic bacterial communities in the phyllosphere have not been characterized. The authors hypothesize that photosynthetic bacteria are common in the phyllosphere and that the growth period of crops will affect community composition. The results are in support of this hypothesis, as 3,150,689 quality-filtered reads were found in 6725 identified OTUs across 35 pooled samples, alpha diversity changed throughout the growth stages of tomato, cucumber, and soybean, and community dissimilarity was affected by plant growth stage. The reviewer finds the manuscript to be technically sound and that the data supports the authors' conclusions.

2. Figures, tables, and captions: The figures are clear and easy to understand, as are the captions.

4. There are no issues with the writing that would detract from understanding the work, save for one instance where clarity is needed.

Lines 50 - 51: This sentence could be reworded; it reads like it is missing a phrase. As written, this sentence implies that photosynthetic bacteria have only been in the phyllosphere as of recently. Is the sentence meant to convey that the existence of photosynthetic bacteria in the phyllosphere was recently confirmed?

Line 54: The phrase "trigger inducible" seems redundant. For example, the literature cited uses the phrase "induces systemic resistance" in the title.

Reviewer #2: The manuscript by Ju-E et al. provides relevant information on changes in bacterial communities within different crop field caused by the different growth periods. However, substantial revision is needed to improve the clarity of the information provided, particularly regarding to the materials and methods, results, and discussion. Additionally, the manuscript should be proofread to improve the quality of the writing. More specific comments are provided below. Please proofread the manuscript to eliminate typos, misplaced words, missing spaces, sentences that need to be restructured to avoid confusion and improve coherence, and formatting errors.

The title of the manuscript is not very clear, it should be like “Metagenomic analysis of dynamical conversion of photosynthetic bacterial communities in different crop fields over different growth periods”.

Page 2, line 33. Please consider to remove “and” from sentence. different 33 crop species and at different growth stages.

Page 2, line 38. Consider to remove “and” among plant growth and development.

Page 3, line 49. “proteobacteria” Be consistent with the use of bacterial name in italic and with the use of capital letters. Check throughout the manuscript.

Page 4, line 82. Add “help to identify” instead of “help reveal”.

Page 5, line 88 and 89. These two sentences are useless in the start, adjust it in the last before DNA isolation and consider it like “a total of 35 samples were collected from leaves of three crops at different growth stages for subsequent microbe isolation and high throughput sequencing process.

Page 5, line 95. The methodology part is lack of crop plantation points, in which base the block were randomly selected? Fertilization/nutrients rate was same in every block? How many seed were cultivated in every block? Was the seed quantity was varied or same per block? After how much time the samples were collected?

Page 5, line 104. This sentence is unclear, please consider to rewrite it.

Page 8, line 151. Consider to mention the quality filtration information of all the 35 samples as a supplementary table.

Page 11, line 223-226. Fig 3C doesn’t representing the mentioned bacterium except few one.

Page 11, line 227. Explain all the significantly diverse bacterial species among different crop at different growth stages.

Page 15, line 269. Table 5, Consider to mentioned all the a, b, c (P-value) along with the tables. Check with every table showing statistical data.

Page 17, line 294-296. The sentence should be like, the results showed that the photosynthetic bacterial community was common in the phyllosphere and the composition of photosynthetic bacterial community at the phylum and genus levels were similar among the growth stages of the three crops.

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Reviewer #1: No

Reviewer #2: No

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Attachments

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Submitted filename: Reviewed by Hafeez.docx

Metagenomic analysis of the dynamical conversion of photosynthetic bacterial communities in different crop fields over different growth periods

PONE-D-21-13677R1

Dear Dr. Zhang,

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,

Suzanne L. Ishaq, PhD

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

Reviewer #2: All comments have been addressed

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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: All previous comments were addressed. However, the additional information provided in the Materials and Methods section does raise additional questions about nutrient application rates and the experimental design.

Materials and methods:

Lines 101-105: More of the experimental design has been added, but the usage of "block" for two different levels is somewhat confusing. Replacing "block" where it appears in Line 101 (referring to the field picked for experimentation) with another term may be helpful.

Line 103: For the sake of experimental replication, the information on nutrient application could be included as supplemental information or be briefly described beyond "The nutrients were consistent."

Lines 103-104: Having this sentence come before the one detailing random assignment of crops to blocks is confusing. It is also not clear that each block is planted in a monoculture. It could help to combine sentences and clarify that each crop was randomly assigned to three replicate blocks and planted in a monoculture of 300 seedlings. Or, a simple diagram could be included.

The manuscript could also benefit from further proofreading and editing for clarity. The following comments are some suggestions along those lines.

Abstract:

Lines 27 - 28: As the sentence is currently written, the apostrophe is no longer needed. Alternatively, the phrase "the knowledge...in field crops" could be replaced with "knowledge of photosynthetic bacterial community dynamics in field crops" to make the first sentence of the abstract more concise.

Line 31: Consider restructuring this sentence to place the growth stages closer to the list of crops being sampled (ex: "...collected from the seedling, flowering, and mature stages of tomato, cucumber, and soybean plants.")

Line 32: Consider replacing "they" with the subject (samples) for clarity

Introduction:

Line 70: Consider moving the verb in this sentence and changing tense. As currently written, the sentence may imply the bacteria no longer have the properties described. (ex: "Methylobacterium spp., the first...bacteria, were found to have..."

Discussion:

In the second sentence, it would help to clarify that these are your results and not results from the aforementioned studies.

Figures:

The color palette may be difficult for people with color deficiencies to view.

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