PONE-D-21-19296

Five decades (1972-2020) of zooplankton monitoring in the upper San Francisco Estuary

PLOS ONE

Dear Dr. Bashevkin,

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.

This manuscript has three reviewers. Among them, two reviewers suggested to reject and one reviewer suggested to accept. Please read all three reviewers' comments in detailed. Please revise this manuscript extremely careful. Particularly, the scientific contributions and many other issues should address in your revision point to point rebuttal letter. I will try to invite different reviewers to have second opinions.

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We look forward to receiving your revised manuscript.

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Jiang-Shiou Hwang, Ph.D.

Academic Editor

PLOS ONE

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Additional Editor Comments (if provided):

This manuscript has three reviewers. Among them, two reviewers suggested to reject and one reviewer suggested to accept. Please read all three reviewers' comments in detailed. Please revise this manuscript extremely careful. Particularly, the scientific contributions and many other issues should address in your revision point to point rebuttal letter. I will try to invite different reviewers to have second opinions.

[Note: HTML markup is below. Please do not edit.]

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: No

Reviewer #3: Partly

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

Reviewer #1: N/A

Reviewer #2: No

Reviewer #3: N/A

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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: No

Reviewer #3: 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

Reviewer #3: 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: The title reminded me of results on a long-term survey on SFE and some kinds of impacts of invasive non-indigenous organisms on the native ecosystem. However, in fact, this is a brief manual and explanation to use the software the authors created. Although separate datasets concerning long-term surveys on SFE are integrated in this, actual outputs should be shown by the authors as suggested in "Data Use and recommendation for reuse" in Discussion. So the authors had better indicate this in the website.

Reviewer #2: While the abstract engages in bragging about how this is the “longest available dataset (by 15 years) of estuarine zooplankton abundance worldwide,” except for 3 figures, the manuscript presents NO DATA on zooplankton patterns! It reads like a technical report to a funding agency rather than a scientific paper. Further, the manuscript is not well-written, particularly for authors who are presumably writing in their first language. Also, the statement that “long-term zooplankton datasets from estuaries are less common” ignores several unmentioned estuarine zooplankton datasets in published papers that should have been cited (see recent issues of Journal of Plankton Research and papers cited therein). In short, this manuscript appears to have been written by authors who are inexperienced in writing scientific papers. While producing the long-term dataset is certainly commendable, its presentation deserves better than this manuscript, which is a disservice to the authors, and their colleagues and predecessors who devoted considerable effort to collecting and analyzing the data.

In terms of writing, there is inconsistency in the hyphenation of double-word adjectives, and the same words, or combinations of words, are frequently presented differently, and often incorrectly (“under sampled” versus “undersampled”, “lifecycle”, “timeseries”). In the tables, abbreviations for surveys should be given in the table legend of each table, not just once in the text. Pronouns that begin sentences (such as “They”) should refer to the last noun used in the previous sentence, not one used before the last noun. Slang such as “lab” instead of “laboratory” should be avoided. Descriptions of sampling methodology should be written in past tense (although the project appears to be ongoing, the data for this manuscript ended in 2020).

The length of the introductory material should be greatly reduced. The Introduction begins on p. 2, with “Background and Motivation” (p. 2-7), “Monitoring overview” (p. 7-10, “Dataset description and access” (p. 10-14), followed by “Methods” (with various subtitles) from p. 14-31. THERE IS NO “RESULTS” SECTION. The manuscript then concludes with sections for “Discussion” (p. 32-34), “References (p. 34-42), and several figures.

Reviewer #3: good and important work to put the different data sets together. In the abstract, line 30, "what make the fishes important?" (commercially important?). Then the UK people have similar data sets from around their islands and inland lakes. And Hawaii has the Hawaii Ocean Time-series (HOT) from their station ALOHA. One day one can find correlations like:

North–South shifts of the Gulf Stream and their climatic connection with the abundance of zooplankton in the UK and its surrounding seas --- Arnold H. Taylor

ICES Journal of Marine Science, Volume 52, Issue 3-4, June 1995, Pages 711–721, https://doi.org/10.1016/1054-3139(95)80084-0

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Reviewer #1: No

Reviewer #2: No

Reviewer #3: No

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Attachments

Attachment

Submitted filename: Bashevkin et al. 2021 PLoS One review.docx

PONE-D-21-19296R1

Five decades (1972-2020) of zooplankton monitoring in the upper San Francisco Estuary

PLOS ONE

Dear Dr. Bashevkin,

Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we have decided that your manuscript does not meet our criteria for publication and must therefore be rejected

I am sorry that we cannot be more positive on this occasion, but hope that you appreciate the reasons for this decision.

Yours sincerely,

Jiang-Shiou Hwang, Ph.D.

Academic Editor

PLOS ONE

[Note: HTML markup is below. Please do not edit.]

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: No

**********

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: Although I understand the value of the paper, I wonder if it is published in an international journal. This paper totally depends on some independent long-term projects. So, as previously mentioned, this is actually a manual to comprehensively deal with previous data. As you suggested at L705-715, could you concretely indicate some kinds of perspectives using this data set?

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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.]

- - - - -

For journal use only: PONEDEC3

PONE-D-21-19296R2Five decades (1972-2020) of zooplankton monitoring in the upper San Francisco EstuaryPLOS ONE

Dear Corresponding author, 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. Pls. also make use in following an amended copy of your submission sent by REVIEWER 4!

Please submit your revised manuscript by Apr 08 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:

• 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: 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,

Hans-Uwe Dahms, 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:

According to REVIEWER 4, pls.:

1. Figure 1. increase the x axis and y axis font size, the sampling points can be more well defined.

2. Include a line or two about the knowledge gap and future recommendations.

3. Rainfall plays huge role in the estuarine ecosystem, why was there no data about rainfall?

[Note: HTML markup is below. Please do not edit.]

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 #4: (No Response)

Reviewer #5: 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 #4: Yes

Reviewer #5: Yes

**********

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

Reviewer #4: Yes

Reviewer #5: 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 #4: Yes

Reviewer #5: 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 #4: Yes

Reviewer #5: 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 #4: PONE-D-21-19296R2 - Five decades (1972-2020) of zooplankton monitoring in the upper San Francisco Estuary

This manuscript presents the dataset of estuarine zooplankton abundance worldwide from 1972-2020. This manuscript is very informative, the background is well written to set the premises of the dataset. The methodology is well explained. I also appreciate the inclusion of micro-zooplankton; these organisms are ecologically important but are often understudied. This dataset will be handy for ecological synthesis and ecosystem modellers. I recommend this manuscript for publication. However, I have some suggestions and queries

1. Figure 1. increase the x axis and y axis font size, the sampling points can be more well defined.

2. Include a line or two about the knowledge gap and future recommendations.

3. Rainfall plays huge role in the estuarine ecosystem, why was there no data about rainfall?

Reviewer #5: Although, one of the reviewers talked about correlating the dataset with climate conditions, which can be done as another work. but I was at least expecting to see an interpretation of the result/data presented, or what the data show.

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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 #4: No

Reviewer #5: Yes: Esther U. Kadiene

[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.]

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Attachments

Attachment

Submitted filename: reviwer comment - PONE-D-21-19296R2.docx

Five decades (1972-2020) of zooplankton monitoring in the upper San Francisco Estuary

PONE-D-21-19296R3

Dear Dr. BASHEVKIN,

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,

Hans-Uwe Dahms, Ph.D.

Academic Editor

PLOS ONE

Additional Editor Comments (optional):

This DATA SET contribution has now reached an ACCEPTABLE level.