PONE-D-21-31328Genome insights from the identification of a Pandoraea sputorum strainPLOS ONE

Dear Dr. Gao,

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Academic Editor

PLOS ONE

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This work was supported by National Key R&D Programme of China (No. 2016YFF0203204) and National Key Technology Research and Development Programme of China (No. 2012BAK11B06) for G.-M. Z. Scientific research project of General Administration of Customs. P. R. China (2021HK171) for Y. W.

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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

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

Reviewer #1: N/A

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Reviewer #1: Yes

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Reviewer #1: Yes

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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: PONE-D-21-31328: Genome insights from the identification of a Pandoraea sputorum strain

The authors describe the relationship between a strain of Pandoraea derived from Phytophthora rubi with some previously described Pandoraea species at the genomic level and conclude that it is likely to belong to the species P. sputorum. They also compare quorum sensing and oxacillinase genes from their strain with those from other species of this genus.

Major comments: While the authors have been quite systematic in their comparison of strain Pandoraea sp. 892iso with other species at the genomic level, they have not included a large number of species which have been added to this genus in the last few years. In addition, while the analysis is thorough, a considerable portion of their manuscript focuses on the description of where this strain sits in the taxonomy of this genus and this seems to be out of proportion with respect to the final conclusion i.e. that this strain belongs to P. sputorum. It would be better if the authors focused less on the where their strain fits in this genus and more on the interesting aspects concerning their quorum sensing and oxacillinase gene comparisons and their MLSA typing approach.

Minor comments:

Please avoid using the word “strain”, unless required, or else preface it with “type” or “reference” where appropriate (for example in the legend for figure 3).

Title:

This should be more informative.

Abstract:

Line 13-would be useful to explain what Phytophthora rubi is.

Line 15: Would be useful to clarify which Pandoraea species you are referring to.

Line 21: Please make it clear which Oomycetes strain you are referring to.

Introduction:

Line 27: Use “genus” rather than “species”

Line 30: Please re-structure this sentence as it is unclear.

Line 33: Many additional species have been added to this genus in the last few years. Please see Peeters et al., (2019) Comparative Genomics of Pandoraea, a Genus Enriched in Xenobiotic Biodegradation and Metabolism.Front. Microbiol. 10:2556 and the following for additional species: Anandham et al., 2010; Sahin et al., 2011; Jeong et al., 2016). Please update your manuscript with this information.

Line 40: “Further”

Line 67: “were identified through whole genome sequencing”

Lines 68 and 75: Please use “isolate” rather than strain

Materials and Methods:

Line 90: Do you mean “calculations” rather than “calculate”?

Line 95 and 100: please clarify what you mean by “11 species”.

Results:

Line 114: Which Pandoraea sputorum isolate are you referring to? If it is Pandoraea sp. 892iso It may be better to use the name of the strain at this stage as the evidence for the WGS-based identification has not yet been presented.

Line 134: It would be helpful if the authors included some details about the types of single copy genes chosen for their generating their phylogenetic tree, with the genes listed in a table, or in supplementary information.

Lines 183-188: The decision to choose these particular house-keeping genes should be explained.

Line 207: A much shorter title to this section should be chosen.

Figures and Tables:

Figure 2: The legend for this figure needs further information about the methods used to generate this data.

Table 1: Please clarify the accession numbers and details for the P. pulmonicola, P. sputorum genomes used, and also for the other species for which this information had not been provided.

Table 2: This table needs some description in the legend, and further details in the main text to explain what it depicts.

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Reviewer #1: No

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PONE-D-21-31328R1Genome insights from the identification of a novel Pandoraea sputorum isolate and its characteristicsPLOS ONE

Dear Dr. Gao,

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, take into consideration all the comments raised by me and the reviewer.

Please submit your revised manuscript by May 21 2022 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:

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• 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,

Paula V Morais, Ph.D

Academic Editor

PLOS ONE

Additional Editor Comments:

1- The number of species of Pandorea is not correct. See https://lpsn.dsmz.de/genus/pandoraea

2- To consider a strain a new species we have 3 criteria and not 2. 16S rRNA gene sequence has to be considered (introduction).

3- What made you suspect that the fungus culture was contaminated? Give some detail (material and methods).

4- You still have the number of Pandorea wrong "...KP771987.1). BLAST was employed to identify homolog genes in the 11 Pandoraea species." Did you repeat the comparison with the 28 Pandorea strains?

5- Please, clarify "...per 1 Mb, which is more/fewer than most of the other sequenced bacteria...."

6- Table 1. What was the criteria to include 30 strains of Pandorea species? What was the criteria for the order they are included? I would like to see them by alphabetic order.

7- "In total, 3,456 849

orthologous genes were shared in common between Pandoraea sp. 892iso and the other four Pandoraea straintypes." Which ones?

8- "fig|93222.8.peg.2650 with the function of ubiquitin in the NR database." Do you mean predicted function?

9- Table 3 and Table 4. List the species by alphabetic order unless you could present a relevant criterium for not doing it.

10- "...AHL receptor protein (ppnR) in Pandoraea sp. 892iso and the nine Pandoraea species are shown..." Why 9 Pandorea species?

11- Table 6. I do not understand. How many genes? How namy species type strains?

12- "...and combined the data with existing genomic data for five other Pandoraea" Is it correct?

13. "It is speculated that Pandoraea sp. 892iso is the endosymbiont of the Phytophthora rubi strain." I do not see in your manuscript any result that supports this sentence. Why the isolate is not a contaminant of your culture? This comment is related with the 3 comment. If you want to include this senetence you have to explain in detail the fungus isolation and culture and the bacteria isolation story.

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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 #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 #2: Yes

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

Reviewer #2: Yes

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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 #2: Yes

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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 #2: Yes

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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 #2: There should be unification for the term that used after Pandoraea. Three different terms (types, sp., and previously strains) were employed throughout the manuscript. The term “species” is usually used in the literature.

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Reviewer #2: No

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PONE-D-21-31328R2

Genome insights from the identification of a novel Pandoraea sputorum isolate and its characteristics

PLOS ONE

Dear Dr. Gao,

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.

Figures 4 and 5 need to be improved so they can be published as supplementary figures. The manuscript has to be revised to be adapted and the figures numbered according.

Please submit your revised manuscript by Jul 18 2022 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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• 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,

Paula V Morais, Ph.D

Academic Editor

PLOS ONE

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Genome insights from the identification of a novel Pandoraea sputorum isolate and its characteristics

PONE-D-21-31328R3

Dear Dr. Gao,

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.

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Kind regards,

Paula V Morais, Ph.D

Academic Editor

PLOS ONE

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