PONE-D-21-32723B.Y.O. Bees: managing wild bee biodiversity in urban greenspacesPLOS ONE

Dear Dr. Del Toro,

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.

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Amparo Lázaro, PhD

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: Yes

Reviewer #2: Yes

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

Reviewer #1: Yes

Reviewer #2: I Don't Know

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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: 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: This paper presents the results of a two-year research evaluating bees in urban and suburban habitats. Urban habitats were both managed and unmanaged ones. Whereas, suburban habitats were exclusively the managed ones. Management was found to increase bee richness and abundance. In my view, this is an overstatement as the unmanaged suburban areas were not subject to an analysis. Thus, this conclusion needs to be made more precise.

Main impressions and journal's standards

Generally, the paper was well written and is very interesting to read. The topic is important for a wide audience and the findings can be quite useful, e.g. for urban planners or natural resource managers. The analysis is mostly sound and the conclusions justified. There are, however, some issues to resolve and I would thus recommend the manuscript for revision before it can be published.

Materials and methods

Management regimes and landscape scale.

Was there a management level, i.e., what % of the area was sown with pollinator-friendly plants? What % of the area was designated to fulfil this criterion? Could you briefly describe what plant species were dominant in the unmanaged habitats? Please, explain why unmanaged suburban areas were not included in the research conducted.

Bee sampling and identification.

Information on the total number of samples taken in each year of the study and in the urban and suburban habitats would be useful.

For the purpose of giving other scientists an idea of the climatic conditions in the research area, please add information on what average temperatures prevail in the area during springtime and summertime period.

Each site was sampled with the pan trap array once every two weeks.....

Define precisely what the trial means to you. The sum of bees caught in all bowls? Was this data merged?

Analyses

Tree species diversity was assessed at each site within a 20m x 20m plot contained within the 30m x 30m pan trap array plot .....

Were the flower colours of woody plants also assessed with the use of colour wheel? Why no assessment of the bee nutrient base in the springtime was conducted? Could you additionally include a list of plants with their assigned flower colours in the appendix?

Results

Bee community response to management styles.

Formulate your conclusions carefully. The sentence above may be misleading as the unmanaged suburban habitats were not included in the research.

Discussion

Although some landscape-level variables were positively associated with wild bee ...

What is the plants base in the springtime like? I am missing this information.

Recommendations for greenspace management.

You should also refer your results to the literature which indicates that the unmanaged habitats are also attractive to wild bees. Unmanaged sites, rich in the floral species also provide stable resources.

Twerd L., Banaszak-Cibicka W. 2019. Wastelands: their attractiveness and importance for preserving the diversity of wild bees in urban areas. Journal of Insect Conservation 23(3): 573–588.

Machon N. 2021. Urban Wastelands Can Be Amazing Reservoirs of Biodiversity for Cities. Urban wastelands 3-18.

McKinney. 2021. Strategies for Increasing Biodiversity Conservation in Cities Using Wastelands: Review and Case Study. Urban wastelands 39-64.

Twerd L., Banaszak-Cibicka W., Sobieraj-Betlińska A., Waldon-Rudzionek B., Hoffmann R. 2021. Contributions of phenological groups of wild bees as an indicator of food availability in urban wastelands. Ecological Indicators 126: 107616.

Reviewer #2: Review for submitted manuscript entitled ‘B.Y.O. Bees: managing wild bee biodiversity in urban greenspaces’.

The manuscript focuses on how wild bee communities are affected by greenspace and landscape-level features in urban greenspaces. How pollinators cope with urbanization is now a very important issue. The subject of the paper is therefore interesting. This is not a new issue, but an additional point of discussion to the current literature. While these results are not especially surprising, they do help policy makers and urban planners by providing compelling evidence for advisability of appropriate urban management for those insects.

My primary concerns with this study have to do with the study design. The paper lacks specific information on methodology. More details about the study sites should be provided. It could be done in the table or in a more descriptive manner. What were the management practices for pollinators, floral diversity, tree diversity on individual sites?

Justification of three study site types selection (managed urban sites, unmanaged urban sites and managed suburban sites) is needed. Why are unmanaged suburban sites missing?

How many samples were collected for each site type?

Add reference to the method floral diversity evaluation at each site.

There are no figures for PCoA analyzes.

Information on bee diversity is missing in the results, but appears in the discussion for the first time in the paper.

“Although habitat fragmentation in urban areas negatively affects bee diversity, we demonstrate that many of these effects can be remedied through the active management greenspaces for wild bees.” - was it analyzed at this paper? I don’t believe that such analyzes are mentioned in the methods section.

Overall, there are several points that need to be changed and improved until this paper is ready for publication.

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Reviewer #1: No

Reviewer #2: No

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PONE-D-21-32723R1B.Y.O. Bees: managing wild bee biodiversity in urban greenspacesPLOS ONE

Dear Dr. Del Toro,

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 have been now reviewed by one of the previous reviewers who is satisfied with the revisions done. I generally agree with the reviewer, but I still think that some extra revisions should be done before the article could be finally accepted for publication.

The main ones are:

• the results for the GLMs are not adequately reported. Apart from giving the estimates and AIC values for the best model, the authors should run likelihood ratio tests (LRT) to give the statistics (i.e. chi square values, df, and p values) for each variable included in the best model and report them either in a table or in the text.
• Line 260-263- if you just omitted them from the analysis you are comparing data from fewer pantraps there that in other places, which could bias the result. You should standardize by subsampling (Gotelli and Colwell 2001) so you have the same number of pantraps to compare everywhere, as typically done. Please either do this subsampling or clearly justify why you do not do it. It does not seem correct to compare places with different sampling effort.

Others:

• add letters for significant differences after post hoc analysis in fig 2. And complete the legend with this.
• Add reference for Shannon diversity index (line 240 )
• Add also a reference in the sentence given in lines 67-69.
• There is abundant literature regarding the effect of floral diversity on bee communities and it should be cited in the discussion section. Same for other parts, the discussion section lacks references to previous work.

Please submit your revised manuscript by Aug 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:

• 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,

Amparo Lázaro, PhD

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.

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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

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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

********** 

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: This paper presents an interesting study on the occurrence bees in urban and suburban habitats. This topic is still understudied, so the authors make an important contribution to recognizing these issues. I am pleased to accept the changes made to the manuscript and recommend publication of this manuscript.

********** 

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

**********

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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.

PONE-D-21-32723R2B.Y.O. Bees: managing wild bee biodiversity in urban greenspacesPLOS ONE

Dear Dr. Del Toro,

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.

Although the authors have done a good effort to include my last comments, the statistical issue is still not resolved and therefore I cannot accept the manuscript for publication yet in its current form. In my previous comment I indicated that the results for the GLMs were not adequately reported. Apart from giving the estimates and AIC values for the best model (which one gets with the function ‘summary’), the authors should run likelihood ratio tests (LRT) to give the statistics (i.e. chi square values, df, and p values) for each variable included in the best model and report them either in a table or in the text. This can be obtained with function ‘Anova’ in library (car) or alternatively with function ‘Drop1’ applied to the best-fitting model. Otherwise we cannot know whether the variables that appear in the best model have a significant effect on the response or not. The authors have conducted two likelihood ratio tests to compare the best-fit GLMs with the global GLMs for both bee abundance and bee species richness, but this is not what I meant them to do.

Another important issue is that I see that in the last revised version the authors have removed a paragraph in the statistical analyses section where the GLMs were explained. Right now, there is no explanation of the GLMs conducted. The authors should explain clearly the statistical analyses conducted (type of model, error distribution, whether it is mixed model or not, predictor and response variables) and also how did they perform model selection (did they use automatic selection with dredge function in MuMIn package? If not, did they try all the possible combinations? How did they  do so?). Lastly, as commented above, the authors may add the LRT to the best-fitting model to show the significance of the variables included in it. Until all these issues are adequately solved I cannot accept the manuscript for publication.

Please submit your revised manuscript by Sep 29 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,

Amparo Lázaro, PhD

Academic Editor

PLOS ONE

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[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.

PONE-D-21-32723R3B.Y.O. Bees: managing wild bee biodiversity in urban greenspacesPLOS ONE

Dear Dr. Del Toro,

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. Although the authors have included the LRT as I indicated, there are a couple of minor issues that should be solved before publication: - in line 339-340, the authors indicate:  'the model’s goodness-of-fit was verified using likelihood ratio tests (Table 2)'. However, LRT do no test model fit, but the significance of the effect of different predictor variables on the response. So this sentence is incorrect. The authors might rather say that the significance of the predictive variables in the best-fitting model was tested using LRT.- Also in the new table 2 with the results of LRT, it might be 3 columns: df, Chi2 and p-values. It is fully correct to say in the legend of the table that these are the results of LRT, but in the column, the value of hte statistics is a value of Chi2 (not LRT). So please, change the heading of the column from LRT to Chi2. Also, p-values should be written adequately, using 3 decimals (or 4 if necessary), and using '< 0.0001' when p-values are smaller than 0.0001.

Please submit your revised manuscript by Dec 25 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,

Amparo Lázaro, PhD

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.

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[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.

B.Y.O. Bees: managing wild bee biodiversity in urban greenspaces

PONE-D-21-32723R4

Dear Dr. Del Toro,

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,

Amparo Lázaro, PhD

Academic Editor

PLOS ONE

Additional Editor Comments (optional):

Reviewers' comments: