Dear Dr. Ducat,

Thank you very much for submitting your manuscript "Predicting partner fitness based on spatial structuring in a light-driven microbial community" for consideration at PLOS Computational Biology. As with all papers reviewed by the journal, your manuscript was reviewed by members of the editorial board and by several independent reviewers. The reviewers appreciated the attention to an important topic. Based on the reviews, we are likely to accept this manuscript for publication, providing that you modify the manuscript according to the review recommendations.

Please prepare and submit your revised manuscript within 30 days. If you anticipate any delay, please let us know the expected resubmission date by replying to this email.

When you are ready to resubmit, please upload the following:

[1] A letter containing a detailed list of your responses to all review comments, and a description of the changes you have made in the manuscript. Please note while forming your response, if your article is accepted, you may have the opportunity to make the peer review history publicly available. The record will include editor decision letters (with reviews) and your responses to reviewer comments. If eligible, we will contact you to opt in or out

[2] Two versions of the revised manuscript: one with either highlights or tracked changes denoting where the text has been changed; the other a clean version (uploaded as the manuscript file).

Important additional instructions are given below your reviewer comments.

Thank you again for your submission to our journal. We hope that our editorial process has been constructive so far, and we welcome your feedback at any time. Please don't hesitate to contact us if you have any questions or comments.

Sincerely,

Pedro Mendes, PhD

Academic Editor

PLOS Computational Biology

Jason Haugh

Section Editor

PLOS Computational Biology

***********************

A link appears below if there are any accompanying review attachments. If you believe any reviews to be missing, please contact ploscompbiol@plos.org immediately:

Reviewer's Responses to Questions

Comments to the Authors:

Please note here if the review is uploaded as an attachment.

Reviewer #1: I liked how the model was calibrated using experimental data. There was a good synergy between experimental and computational techniques. I also appreciate the python code for processing of the NUFEB results.

Minor comments below:

Line 171: Is it mu or mu_i?

Lines 186-189: For equations 5-8, psi is used instead of psi_i, is there a difference? If yes, what is the formula for psi?

Line 282: Are there links to the custom models mentioned? Or sample NUFEB input files?

Line 305: Did you mean sucrose biomass accumulated?

Line 339: It is unclear how fig. 4B shows the negative correlation.

Reviewer #2: In the manuscript “Predicting partner fitness based on spatial structuring in a light-driven microbial community, the authors posed a computational IBM using a published platform NuFeb and parametrized with experimental data of Synechococcus elongatus a sucrose-secreting strain and Escherichia coli W that can use sucrose as a carbon source. Authors find that initial biomass and distance from the E coli colonies are the main parameters to establish successful consortia.

This is a good example of how simulations, particularly IbM models, can help us understand and predict how synthetic microbial consortia can be established; it is interesting how the author adapts the IbM model to explore these consortia, and I think it could be of interest of the academic community.

Some comments.

1.- Parameters were obtained from experimental data but in different culture conditions (different media). This is problematic for the parameterization and the prediction of establishing a stable consortium. If these two strains have already proven to form a consortium, why not grow them in the same media culture?

2.- The authors talk about the stability of natural consortia. As the simulations run to a steady state. It would have been interesting to subject the simulations to a change of environment, to challenge this stability. Can this be done on this platform?

3.- For measurements and validation of the IBM model, how many cells are in each experiment? 11 OD is a very high measurement; this could easily measure with a flow cytometer and correlated with the total number of cells in the computational simulation. These results could be relevant as the prediction from the model is that initial density is a determinant in the establishment of the consortia and also the accumulation of sucrose is also an important factor.

4.- If E coli utilize far more sucrose than S. elongatus can produce, do the authors obtain conditions by which there is competitive exclusion?

5.- I think the discussion could be improved by discussing how to integrate the findings in real experiments, as it has already been published that these two strains can be co-culture.

6.- A flask with constant shaking is usually used as a proximation of a homogeneous environment; why is it a spatial environment? Does any of these strains form spatially structured formations as biofilms? Consortia can survive in a homogenous environment, or if sucrose can diffuse further?

7.- In terms of total biomass (both strains), what conditions maximize it?

There is a trade-off between the secretion of sucrose ( high concentration of IPTG) and the growth of S. elongatus, so is there an optimal secretion rate?

Reviewer #3: The authors put together a novel experimental and computational analysis of a spatial microbial community. This is a very interesting paper and I think will be of interest to the Plos Comp bio community.

The authors used experiments to calibrate their individual based model and determined the importance of spatial organization towards predicting colony fitness.

Major Questions:

(1) One major question the author's sought to investigate how well fitness could be predicted. While I believe the authors have explained many of their technical details, I found it difficult - with the ordering of sections in their manuscript - to understand what they meant by "fitness"?

This is because it wasn't until page 20 (line 375) that the authors state "aggregate colony fitness (total biomass at the end of the simulation".

(2) I found it very interesting that the Voronoi tessellation area (aka the growth potential) for a given colony was a poor predictor of fitness (which I'm now interpreting as total colony biomass). Presumably this would not be the case for a different type of microbial species interaction?

(3) While the authors did an excellent job of using their framework in a specific context, it would be helpful for the readers if the authors could speak a bit more broadly about how this work might generalize to other types of microbial interactions? Or indeed would all future study require the same detailed fine-tuning the authors performed here?

Minor Edits:

- When equations end sentences, they should have a period after them. Periods are missing on Equations (12)-(17)

**********

Have the authors made all data and (if applicable) computational code underlying the findings in their manuscript fully available?

The PLOS Data policy requires authors to make all data and code 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 and code 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 or code —e.g. participant privacy or use of data from a third party—those must be specified.

Reviewer #1: No: Sample input files of the custom models haven't been provided.

Reviewer #2: Yes

Reviewer #3: Yes

**********

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

Reviewer #3: No

Figure 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. 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 us at figures@plos.org.

Data Requirements:

Please note that, as a condition of publication, PLOS' data policy requires that you make available all data used to draw the conclusions outlined in your manuscript. Data must be deposited in an appropriate repository, included within the body of the manuscript, or uploaded as supporting information. This includes all numerical values that were used to generate graphs, histograms etc.. For an example in PLOS Biology see here: http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.1001908#s5.

Reproducibility:

To enhance the reproducibility of your results, we recommend that you deposit your laboratory protocols in protocols.io, where a protocol can be assigned its own identifier (DOI) such that it can be cited independently in the future. Additionally, PLOS ONE offers an option to publish peer-reviewed clinical study protocols. Read more information on sharing protocols at https://plos.org/protocols?utm_medium=editorial-email&utm_source=authorletters&utm_campaign=protocols

References:

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.

Dear Dr. Ducat,

We are pleased to inform you that your manuscript 'Predicting partner fitness based on spatial structuring in a light-driven microbial community' has been provisionally accepted for publication in PLOS Computational Biology.

Before your manuscript can be formally accepted you will need to complete some formatting changes, which you will receive in a follow up email. A member of our team will be in touch with a set of requests.

Please note that your manuscript will not be scheduled for publication until you have made the required changes, so a swift response is appreciated.

IMPORTANT: The editorial review process is now complete. PLOS will only permit corrections to spelling, formatting or significant scientific errors from this point onwards. Requests for major changes, or any which affect the scientific understanding of your work, will cause delays to the publication date of your manuscript.

Should you, your institution's press office or the journal office choose to press release your paper, you will automatically be opted out of early publication. We ask that you notify us now if you or your institution is planning to press release the article. All press must be co-ordinated with PLOS.

Thank you again for supporting Open Access publishing; we are looking forward to publishing your work in PLOS Computational Biology. 

Best regards,

Pedro Mendes, PhD

Academic Editor

PLOS Computational Biology

Jason Haugh

Section Editor

PLOS Computational Biology

***********************************************************