PONE-D-23-01800Description and genome-wide analysis of <profundicola chukchiensis=""> gen. nov., sp. nov., marine bacteria isolated from bottom sediments of the Chukchi Sea</profundicola>PLOS ONE

Dear Dr. Isaeva,

Thank you for submitting your manuscript to PLOS ONE. As your manuscript (ms) currently stands it does not does not fully meet PLOS ONE’s publication criteria and I have decided to label it as in need of "minor revisions". Therefore, we invite you to submit a revised version of the manuscript that addresses the points raised during the review process.

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Luis Angel Maldonado Manjarrez, Ph.D.

Academic Editor

PLOS ONE

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2. We noticed you have some minor occurrence of overlapping text with the following previous publication(s), which needs to be addressed:

https://www.frontiersin.org/articles/10.3389/fmicb.2019.02083/full

https://www.biorxiv.org/content/biorxiv/early/2019/01/16/522367.full.pdf

https://assets.researchsquare.com/files/rs-1570742/v1/6e265435-68da-4e74-9de0-42402259da79.pdf?c=1650639680

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“This work was supported by a grant from the Ministry of Science and Higher Education, Russian Federation 15.BRK.21.0004 (Contract No. 075-15-2021-1052).”

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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: Partly

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

Reviewer #1: N/A

Reviewer #2: N/A

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3. Have the authors made all data underlying the findings in their manuscript fully available?

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Reviewer #1: Yes

Reviewer #2: No

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Reviewer #1: Yes

Reviewer #2: 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: A new genus Profundicola chukchiensis gen. nov., sp. nov., was described basend on genome taxonomy.

Only bifurcating tree reconstruction is unlikely to show monophyletic association to the ohter related taxa.

Authors should perform splits decomposition analysis to cleary show the monophyly of the strains described here.

major

1. 16S rRNA phylogeny must be shown using ML after model tests.

2. MLSA using splitstree network must be performed.

minors

1. title was not correspoded between in manuscript and submision system.

2. L8. please put and before the last author name.

3. L27 and etc. please correct the font "K"MM p724T.

4. L32 and etc. one digit for similarity, ANI, AAI, and DDH should be used.

5. L54. m not meter.

6. L107. seawater.

7. L141. 16S rRNA gene sequencing.

8. L282. non-motile.

9. Fig. 4. general title should be added.

10. Table 1. capitalized firts letter of feature. no vertical and horizontal sublines.

Reviewer #2: This manuscript describes the isolation of two Gram-negative bacterial strains, which based on 16S rRNA gene sequence analysis could be assigned as members of the Weeksellaceae family. Further analyses provided evidence for the classification of the strains as members of a novel genus, with the two strains described, representing a novel species within this genus. The authors provided a report on the extensive analyses of the strains and their associated genomic features, further providing evidence for the proposed classification. However, there are some aspects the authors need to consider/address:

1. Lines 67-70: The list of the members belonging to the family Weeksellaceae needs to be updated – please see LPSN.dsmz.de for a more complete list.

2. Lines 101, 106, 362: For any % solution reported, please indicate what it represents, i.e., v/v or w/v, etc.

3. Line 110: Please indicate whether an artificial sea water (ASW) control was setup for the API analyses, especially since the strains were suspended in ASW as indicated.

4. Line 148: BLAST analysis and EzBioCloud analysis were performed in 2021. Please indicate whether the same results were obtained during a more recent (2023) search? Sequence information in databases is growing at a phenomenal rate – a more recent analysis would be more accurate.

5. Lines 187-189: dbCAN2 has been updated to dbCAN3 – it would be of value to re-run the genome sequences on the updated version in order to confirm whether the outputs are the same or whether the updated version changes the results presented. dbCAN3 output files should also ideally be downloaded and made available via a data repository.

6. Lines 195-196: Please provide the scripts used for the analyses in R – either as supplementary material or made accessible via a data repository.

7. Line 200: Even though the genome sequence accession numbers are provided, neither provide a hit in GenBank. The same applies to ‘OP604014’. Only ‘LC379507’ returns a result in GenBank for a Flavobacteriaciae bacterium Ch26. Please update the GenBank entry to correspond to what is being reported in the manuscript and ensure that the data linked to the other accession numbers are released. Not being able to access the genomes, made it difficult to assess whether what was reported in the manuscript is reproducible.

8. Minor: Please correct the spelling of ‘source’ in line 349, and ‘designed’ in line 26 should be ‘designated’.

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Reviewer #1: No

Reviewer #2: No

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Description and genome-wide analysis of Profundicola chukchiensis <profundicola chukchiensis="">gen. nov., sp. nov., marine bacteria isolated from bottom sediments of the Chukchi Sea

PONE-D-23-01800R1</profundicola>

Dear Dr. Isaeva,

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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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,

Luis Angel Maldonado Manjarrez, Ph.D.

Academic Editor

PLOS ONE

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Additional Editor Comments (optional):

Please make the following changes and pay attention to the last comment entitled "Final comment".

Minor changes

1. Line 67. It says “has been proposed to include genera”, change to “has been proposed to include the genera”

2. Line 74. It says “During a studying the biodiversity of bacteria isolated”, change to “During a study on the bacterial biodiversity”

3. Line 76. It says “were found”, change to “were recovered”

4. Line 77. It says “methods, and results obtained are”, change to “methods; the results obtained are”

5. Line 78. It says “reported in the present study.”, change to “reported in this study.”

6. Line 100. It says “Gram-staining, oxidase, and catalase reactions, and”, change to “Gram-staining, oxidase, catalase reactions, and”

7. Line 162. It says “and sequenced was performed subsequently using”, change to “and subsequently sequenced using”

Final comment

Perhaps a small paragraph regarding the phylogenetic relationship found between your proposed novel genera (ie. Profundicola) and the poultry pathogen, Ornithobacterium rhinotracheale should be added but should be carefully written.

Some colleagues while reading your manuscript (ms) may well argue a “possible” relationship between the two genera, namely a non-pathogenic (Profundicola) and a pathogenic one (Ornithobacterium). Personally, I find very interesting the phylogenetic relationship found in your ms, but at the same time, the lack of any “ecological-environmental” relationship between the putative origin of isolates belonging to each genera. This raises novel questions regarding the source of infection for poultry: can the sea then also be a reservoir for such pathogenic species? How do birds get the infection? Is there any other relationship -except for the phylogenetic one- between the species of the two genera (as mentioned above either ecologically and/or environmentally)?

You can also avoid including this proposed paragraph but perhaps in the future you and the colleagues involved in the ms might well encounter some criticism based on the points I have tried to raise in this final commentary so it may well be worth to have (or start thinking of) a proper answer at any given time.

I should emphasise that the inclusion or the exclusion of the paragraph I suggest does not affect/change my decision as academic editor on accepting your ms as currently stands.

Best regards,

Dr LA Maldonado

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Reviewers' comments:

No second round of reviewers were needed since all the first round of comments/suggestions were followed accordingly on their rebutal letter.