Metabolic multireactor: Practical considerations for using simple oxygen sensing optodes for high-throughput batch reactor metabolism experiments

Matthew H. Kaufman; Joshua Torgeson; James C. Stegen

doi:10.1371/journal.pone.0284256

Peer Review History

Original SubmissionMarch 8, 2023
3 May 2023 Decision Letter - Catarina Leite Amorim, Editor PONE-D-23-06927Metabolic Multireactor: practical considerations for using simple oxygen sensing optodes for high-throughput batch reactor metabolism experimentsPLOS ONE Dear Dr. Kaufman, 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. The manuscript presents an alternative incubation setup that enables to measure the oxygen consumption in multiple reactors simultaneously. Overall, the study is a valuable contribution to the field and it has potential for wide applicability in other fields. Nevertheless, the authors are encouraged to improve the manuscript following the reviewers recommendations which will help to improve the quality and significance of the work presented. Please submit your revised manuscript by %DATE_REVISION_DUE%. 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, Catarina Leite Amorim, Ph.D. Academic Editor PLOS ONE Journal Requirements: When submitting your revision, we need you to address these additional requirements. 1. Please ensure that your manuscript meets PLOS ONE's style requirements, including those for file naming. The PLOS ONE style templates can be found at https://journals.plos.org/plosone/s/file?id=wjVg/PLOSOne_formatting_sample_main_body.pdf and https://journals.plos.org/plosone/s/file?id=ba62/PLOSOne_formatting_sample_title_authors_affiliations.pdf 2. We note that the grant information you provided in the ‘Funding Information’ and ‘Financial Disclosure’ sections do not match. When you resubmit, please ensure that you provide the correct grant numbers for the awards you received for your study in the ‘Funding Information’ section. 3. Please expand the acronym “PNNL LDRD” (as indicated in your financial disclosure) so that it states the name of your funders in full. This information should be included in your cover letter; we will change the online submission form on your behalf. 4. Thank you for stating the following in the Acknowledgments Section of your manuscript: "..A portion of the research described in this paper was conducted under the Laboratory Directed Research and Development Program at Pacific Northwest National Laboratory, a multi-program national laboratory operated by Battelle for the U.S. Department of Energy. MK was grateful for the support of the Linus Pauling Distinguished Postdoctoral Fellowship program. This research was supported by the U.S. Department of Energy, Office of Science, Office of Biological and Environmental Research, Environmental System Science (ESS) Program. This contribution originates from the River Corridor Scientific Focus Area (SFA) project at Pacific Northwest National Laboratory (PNNL). This research was supported under award DESC0018042." We note that you have provided funding information that is not currently declared in your Funding Statement. However, funding information should not appear in the Acknowledgments section or other areas of your manuscript. We will only publish funding information present in the Funding Statement section of the online submission form. Please remove any funding-related text from the manuscript and let us know how you would like to update your Funding Statement. Currently, your Funding Statement reads as follows: "A portion of the research described in this paper was conducted under the Laboratory Directed Research and Development Program at Pacific Northwest National Laboratory, a multi-program national laboratory operated by Battelle for the U.S. Department of Energy. MK was grateful for the support of the Linus Pauling Distinguished Postdoctoral Fellowship program. This research was supported by the U.S. Department of Energy, Office of Science, Office of Biological and Environmental Research, Environmental System Science (ESS) Program. This contribution originates from the River Corridor Scientific Focus Area (SFA) project at Pacific Northwest National Laboratory (PNNL). This research was supported under award DESC0018042. The sponsors and funders did not play any role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript." Please include your amended statements within your cover letter; we will change the online submission form on your behalf. 5. Thank you for stating the following in your Competing Interests section: "No" Please complete your Competing Interests on the online submission form to state any Competing Interests. If you have no competing interests, please state ""The authors have declared that no competing interests exist."", as detailed online in our guide for authors at http://journals.plos.org/plosone/s/submit-now This information should be included in your cover letter; we will change the online submission form on your behalf. 6. In your Data Availability statement, you have not specified where the minimal data set underlying the results described in your manuscript can be found. PLOS defines a study's minimal data set as the underlying data used to reach the conclusions drawn in the manuscript and any additional data required to replicate the reported study findings in their entirety. All PLOS journals require that the minimal data set be made fully available. For more information about our data policy, please see http://journals.plos.org/plosone/s/data-availability. Upon re-submitting your revised manuscript, please upload your study’s minimal underlying data set as either Supporting Information files or to a stable, public repository and include the relevant URLs, DOIs, or accession numbers within your revised cover letter. For a list of acceptable repositories, please see http://journals.plos.org/plosone/s/data-availability#loc-recommended-repositories. Any potentially identifying patient information must be fully anonymized. Important: If there are ethical or legal restrictions to sharing your data publicly, please explain these restrictions in detail. Please see our guidelines for more information on what we consider unacceptable restrictions to publicly sharing data: http://journals.plos.org/plosone/s/data-availability#loc-unacceptable-data-access-restrictions. Note that it is not acceptable for the authors to be the sole named individuals responsible for ensuring data access. We will update your Data Availability statement to reflect the information you provide in your cover letter. 7. We note that you have stated that you will provide repository information for your data at acceptance. Should your manuscript be accepted for publication, we will hold it until you provide the relevant accession numbers or DOIs necessary to access your data. If you wish to make changes to your Data Availability statement, please describe these changes in your cover letter and we will update your Data Availability statement to reflect the information you provide. [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: Yes Reviewer #2: Yes ******** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes Reviewer #2: No ****** 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 ****** 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 ****** 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 manuscript entitled "Metabolic Multireactor: Practical Considerations for Using Simple Oxygen Sensing Optodes for High-throughput Batch Reactor Metabolism Experiments," authored by Kaufman and colleagues, introduces a novel incubation setup that enables simultaneous measurement of oxygen consumption in multiple reactors. The authors conducted meticulous testing of the system and provided comprehensive supplementary information, including all CAD designs. Overall, the study presents a valuable contribution to the field and showcases the potential of this methodology for high-throughput batch reactor metabolism experiments. The proposed system has the potential for wide applicability in various fields of research, including marine, aquatic, and terrestrial studies. This broad scope of potential applications makes the manuscript an appealing read for a broad readership, and its suitability for publication in PLOS ONE is evident. As the reviewer, I have opted for a "major revision" decision, as I believe there is room for improvement in certain sections of the manuscript. Including these clarifications will improve the overall clarity and understanding of the experimental design. Reviewer #2: The manuscript by Kaufman et al details their development of a microbioreactor system with integrated oxygen measurements via optodes. The authors describe their system (with appropriate supporting information to enable fabrication) and the extensive calibration and determination of system parameters. Important for a paper of this type, the methods section is very clearly written with a suitable amount of detail - one of the best written methods section I've reviewed recently. Overall, all of the experiments the authors completed to analyze their system are appropriate, and the overall presentation of the work is excellent. While I have some minor concerns and suggestions (detailed below), the manuscript is certainly suitable for publication with some minor changes (the most important being incorporation of statistical tests to assay significance of differences) and I look forward to it's publication. Minor Issues & Suggestions - Several sections would benefit from statistical analysis. Basically anywhere where different conditions are being compared (e.g. fig 3, fig 4, fig 5c, possibly fig 6, fig 7, fig 8, some SI figures, and accompanying test. Just doing a comparison and adding if it is significant or not would help to clarify. E.g. - p19 - "reports approximately 4% lower values" but I would guess not significantly different. - Probably worth changing "fluorescent dye" etc. to luminescent given the mechanism for the dyes - Possibly worth cutting 2.5.7 and 2.5.8 from the methods section and integrating into the results and discussion. Not much actual "methods" and more explanation as for motivation. - Figure 5 - possibly add labels to figure (e/g. "autoclaved""not autoclaved" to image) to help make it easier to understand at a glance - P17 (section 3.1.4) "shows that the oxygen permeability into the reactors is low" - add range for what "low" is or explain to the readers. I.e. maybe worth comparing with normal units and show that it is considered low? - Figure 6 (and other may benefit too) - smaller data points to show individual points more clearly. - Section 3.1.5 mentions click chemistry detailed in methods, but I didn't see it there (may have just missed it). - Probably not worth it, but maybe comparing with a different camera type in addition to a duplicate camera would add value for the reader (i.e. same camera - calibration probably fine, different camera - new calibration needed). - ****** 6. 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 ******** [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. Attachments Attachment Submitted filename: review_Kaufmann.pdf https://doi.org/10.1371/journal.pone.0284256.r001
Revision 1
12 Jun 2023 Author Response Dear PlosONE staff and reviewers, We greatly appreciate the time and energy put into the review process for this manuscript. Below please reviewer comments and our responses. Reviewers' comments: Reviewer #1: The manuscript entitled "Metabolic Multireactor: Practical Considerations for Using Simple Oxygen Sensing Optodes for High-throughput Batch Reactor Metabolism Experiments," authored by Kaufman and colleagues, introduces a novel incubation setup that enables simultaneous measurement of oxygen consumption in multiple reactors. The authors conducted meticulous testing of the system and provided comprehensive supplementary information, including all CAD designs. Overall, the study presents a valuable contribution to the field and showcases the potential of this methodology for high-throughput batch reactor metabolism experiments. The proposed system has the potential for wide applicability in various fields of research, including marine, aquatic, and terrestrial studies. This broad scope of potential applications makes the manuscript an appealing read for a broad readership, and its suitability for publication in PLOS ONE is evident. As the reviewer, I have opted for a "major revision" decision, as I believe there is room for improvement in certain sections of the manuscript. Including these clarifications will improve the overall clarity and understanding of the experimental design. We thank the reviewer for their in-depth review and constructive criticism. General comments 1. Heterogeneity measurements: In the introduction, the authors discuss the importance of heterogeneity measurements, which I completely agree with. In my opinion, the proposed system has an key advantage that is currently not addressed: it can directly resolve heterogeneity on the micrometer to millimeter scales. By imaging the roughly 2 cm dye spots, the authors can extract information about the variability of the sensor-dye. This approach would only require determination of the minimum resolvable spatial resolution. We have added information on resolution to the end of the imaging system methods section. Also in the “multireactor advantages” section, the ability to asses heterogeneity was added. Digging into specific statistics/methods for this will be a nice topic for a future manuscript. 2. Improve precision through higher temporal resolution: The manuscript does not explore the potential benefits of increasing the temporal resolution of the readouts to enhance the accuracy of rate measurements. This is an interesting avenue for future research that could be discussed or acknowledged within the manuscript. By improving the temporal resolution of the system, researchers may be able to obtain more precise measurements of metabolic rates (for comparison doi.org/10.1371/journal.pone.0089369 ). Additional discussion of this aspect of higher-frequency sampling has been added to the fourth “Multireactor Advantages” paragraph, as has the provided useful reference. 3. IR blocking: For the applied sensor-dye (PtTFPP) the IR blocking is not really important, as most of the emission is occurring in the lower red range (600 nm – 680 nm). This might however change for other dyes that are utilized by the community. This should be clarified and the sections on the IR blocking should be toned down. We have added the specification that the IR filter section only applies to the specific dye cocktail used in these experiments, and is likely not be applicable to other dyes, to section 3.1.7. 4. Terminology: Throughout the manuscript, the author uses terms such as "metabolism of organic material," "microbial metabolism", "aerobic metabolism", "microbial respiration", and "consumption" interchangeably, despite the fact that these terms describe different processes. While the measurements obtained are primarily oxygen consumption measurements, which integrate a range of processes, including microbial respiration and oxidation of reduced material. It is important to clearly describe this link between organic carbon remineralization and oxygen respiration in the introduction and use consistent terminology throughout the manuscript. I recommend to use "oxygen consumption," to accurately reflect the measurements obtained and avoid confusion. We have reduced the range of terms used to “oxygen consumption” and “metabolism”. We have also added a few lines in the introduction to discuss the non-metabolic contributors to oxygen consumption rates. “Aerobic metabolism rates are frequently reflected in oxygen consumption rates, although inorganic carbon remineralization and abiotic reoxidation of reduced species can also contribute to oxygen consumption rates.” 5. Calibration: The authors are performing and describing in detail the calibration procedure, however the Stern-Volmer equations are missing and should be integrated in the method section then it also becomes clearer to which parameter the authors are referring in table 1. We have added the modified version of the Stern-Volmer equation used by Larsen et. al. [2014] to the methods section (now equation 1), including definitions of the variables referred to in table 1. In my opinion the limit of detection (1.1%) is very conservative and it does not reflect the actual data (Figure 9, Zoom into 0-0.6 mg/L and add the 1.1% line). We have added a statement to section 3.1.5 stating that these limits appear to be conservative, and additional performance may be achievable on an experiment-specific basis. 6. Literature: The reference list is relatively short and does not reflect the breadth of research in this field. The proposed system has the potential to be applied in various environments, including marine, aquatic, and terrestrial studies. Therefore, it would be beneficial for the authors to expand their literature review and include more relevant studies. Additionally, some recent novel developments have addressed heterogeneity on the micrometer scale, which should also be considered in the manuscript.: doi.org/10.1016/j.crmeth.2022.100216 We have added several references to the introduction, both in the optode section and the existing metabolic research section. There is a huge quantity of literature in these fields, so we are necessarily limited in the scope of what we can site for context here. Line and figure specific comments Figures: To reduce the total number of figures in the manuscript, I recommend combining multiple panels into a single figure. Rather than presenting each panel as a separate figure, combining them will simplify the presentation and make it easier for readers to follow the results. This approach will also reduce the total number of figures, making the manuscript more concise and easier to navigate. Figure 1 and figure 2 can be combined. Add scale bar to figure 1 (panel bottom left). Figures 1 & 2 have been combined into a single figure. All figure numbers have been updated througout the manuscript. Abstract: The abstract could be restructured for better clarity. It may be more effective to begin with the importance/introduction and limitations of current systems, followed by the setup and advantages of the proposed system. Also, it may not be necessary to include the reference to Larsen et al.. Instead, it could be stated that ratio-metric sensor-dyes are used, along with the names of the specific dyes. We appreciate this comment, however we prefer to keep the abstract ordered the way it is, with the system and its advantages listed first, and without the methodological details of the ratiometric dyes and dye names. We believe that this provides a concise and accurate description of the manuscript, and further details are readily available in the body. Line 32: See general comment 4 Please see response to general comment 4. Line 46: The authors should give examples of such “whole-system approaches” Several references to “whole system” approaches are provided at lines 42-43, however we have added a bit more explanation of those types of experiments. “Such studies are often approached either through open-water whole-system approaches based on oxygen time series data…” Line 52: The authors should describe what is meant with “manipulative experiments” We have added a line or 2 of explanation at that location. “(that is, experiments where a system is intentionally subjected to a specific set of conditions, rather than an experiment where field conditions are left largely uncontrolled)” Line 62: The reference [11] seems to not reflect the statements made. We have removed the reference from that location. It was intended as an example of one of the “best existing solutions”, but it was not a great example of the difficulties experienced trying to carry out these kinds of experiments. Line 69-70: I disagree to the statement that optodes are traditionally “used to obtain two-dimensional data”. Traditionally optodes are used in the context of microsensors ( doi.org/10.1016/S0925- 4005(97)80168-2 ) We have added some brief discussion of optode microsensors and related studies to this section. Line 118: Effects of bleaching can also be reduced, calibration is improved, etc. pp. Further, while I agree that it is not necessary to provide an in-depth description of the dyes and their chemical properties, it is important to mention which reference dye was used in the manuscript. Additionally, the distinction between the antenna and reference dyes could be clarified for readers. It is the same dye, but the reference dye also serves as an antenna dye, facilitating energy transfer. Also write out once for what PtTFPP actually stands for. We have added the reference/antenna dye name to the methods section. PtTFPP is defined in line 109. We have added a brief statement about the dual role of the Macrolex Yellow GN antenna/reference dye, but we leave most of the details of that system to the cited Larsen paper. Line 274: It is rather the “variability” then the “variance” that is testes corrected Line 337: The wording (“Lifetime test”) is a bit confusing as the lifetime of the quenching can also be used for calibration. This is a good catch. We have changed the term used to “longevity” to prevent confusion. Line 465: The authors are very conservative with their statements regarding how inexpensive their system is. Commercial solutions for similar 4-channel modules are substantially more expensive, such as the Pyroscience system, which costs approximately $10,000 and that does not include any of the spots and additional lab equipment (and allows only the read-out of 4 spots). It may be worth making stronger statements regarding the cost-effectiveness of the proposed system in comparison to existing commercial solutions. We have added a sentence to that section mentioning how expensive commercial multi-point oxygen sensor systems are. Reviewer #2: The manuscript by Kaufman et al details their development of a microbioreactor system with integrated oxygen measurements via optodes. The authors describe their system (with appropriate supporting information to enable fabrication) and the extensive calibration and determination of system parameters. Important for a paper of this type, the methods section is very clearly written with a suitable amount of detail - one of the best written methods section I've reviewed recently. Overall, all of the experiments the authors completed to analyze their system are appropriate, and the overall presentation of the work is excellent. While I have some minor concerns and suggestions (detailed below), the manuscript is certainly suitable for publication with some minor changes (the most important being incorporation of statistical tests to assay significance of differences) and I look forward to it's publication. We thank the reviewer for their in-depth review and constructive criticism. Minor Issues & Suggestions - Several sections would benefit from statistical analysis. Basically anywhere where different conditions are being compared (e.g. fig 3, fig 4, fig 5c, possibly fig 6, fig 7, fig 8, some SI figures, and accompanying test. Just doing a comparison and adding if it is significant or not would help to clarify. E.g. - p19 - "reports approximately 4% lower values" but I would guess not significantly different. This is a great suggestion. We used a Kolmogorov-Smirnov test to determine if any pair of calibrations (“base” and “treatment”) were significantly different. We have added a few lines to the end of the methods section describing the statistical method used, and added the results of those tests to sections 3.1.1, 3.1.2, 3.1.3, and 3.1.6. In all cases (as the reviewer expected) the statistics backed up the existing conclusions. - Probably worth changing "fluorescent dye" etc. to luminescent given the mechanism for the dyes We appreciate this suggestion; however the commercial optical oxygen sensors are predominantly referred to as “fluorescent”. As such, we prefer to stick with that term to hopefully make it easier for domain scientists to find our work. - Possibly worth cutting 2.5.7 and 2.5.8 from the methods section and integrating into the results and discussion. Not much actual "methods" and more explanation as for motivation. We have moved the “motivation” aspects of 2.5.7 to results and discussion section 3.1.7. We have left 2.5.8 as it was, since it does describe the process for creating direct-coated vials, though not in a great deal of detail. - Figure 5 - possibly add labels to figure (e/g. "autoclaved""not autoclaved" to image) to help make it easier to understand at a glance Labels differentiating the “autoclaved” and “not autoclaved” optodes have been added to the figure. - P17 (section 3.1.4) "shows that the oxygen permeability into the reactors is low" - add range for what "low" is or explain to the readers. I.e. maybe worth comparing with normal units and show that it is considered low? Rather than provide normal units for permeability and compare to specific materials (we feel that this would not provide much actionable information), we have added text to explain that we mean “low” in the context of the oxygen consumption rates that are likely to be measured with this system, and some more discussion about when oxygen permeability is likely to be a concern: “In general, Table 2 shows that oxygen permeability into the reactors is low relative to many of the oxygen consumption rates reported in environmental studies, and in many experimental setups dealing primarily with higher oxygen concentrations, faster consumption rates, and/or shorter experiment times it may be safe to ignore entirely. This is less likely to be the case in systems with very low oxygen concentrations and/or very low oxygen consumption rates.” - Figure 6 (and other may benefit too) - smaller data points to show individual points more clearly. The data points in figure 6 have been made smaller. - Section 3.1.5 mentions click chemistry detailed in methods, but I didn't see it there (may have just missed it). This was not explained clearly. The click-chemistry process is only provided via reference in the methods section, not detailed in this manuscript. To make this clearer, we have revised the sentence in 3.1.5 and replicated the pertinent reference there. “performance is likely available either by using the Click-chemistry dye process referred to in the methods section” - Probably not worth it, but maybe comparing with a different camera type in addition to a duplicate camera would add value for the reader (i.e. same camera - calibration probably fine, different camera - new calibration needed). This is a great suggestion; however it is beyond the scope of this manuscript. We have added a line in the Summary, Limitations, and Next Steps section to indicate that evaluation variation between different camera manufacturers and models would be useful. Attachments Attachment Submitted filename: kaufmanetall_MM_2023_response_to_reviewers.docx https://doi.org/10.1371/journal.pone.0284256.r002
22 Jun 2023 Decision Letter - Catarina Leite Amorim, Editor Metabolic Multireactor: practical considerations for using simple oxygen sensing optodes for high-throughput batch reactor metabolism experiments PONE-D-23-06927R1 Dear Dr. Matthew Kaufman, 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. An invoice for payment will follow shortly after the formal acceptance. To ensure an efficient process, please log into Editorial Manager at http://www.editorialmanager.com/pone/, click the 'Update My Information' link at the top of the page, and double check that your user information is up-to-date. If you have any billing related questions, please contact our Author Billing department directly at authorbilling@plos.org. 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, Catarina Leite Amorim, Ph.D. Academic Editor PLOS ONE Additional Editor Comments (optional): All comments have been carefully addressed by authors, improving the manuscript quality and significance. Reviewers' comments: Reviewer's Responses to Questions Comments to the Author Reviewer #1: All comments have been addressed Reviewer #2: All comments have been addressed ******** 2. Is the manuscript technically sound, and do the data support the conclusions? Reviewer #1: Yes Reviewer #2: Yes ****** 3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes Reviewer #2: 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 Reviewer #2: 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 Reviewer #2: 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: The authors have adressed all my comments. I would like to congratulate the authors once more for this nice method and I am looking forward to see future outcomes. Reviewer #2: (No Response) ****** 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 Reviewer #2: No ******** https://doi.org/10.1371/journal.pone.0284256.r003
Formally Accepted
3 Jul 2023 Acceptance Letter - Catarina Leite Amorim, Editor PONE-D-23-06927R1 Metabolic Multireactor: practical considerations for using simple oxygen sensing optodes for high-throughput batch reactor metabolism experiments Dear Dr. Kaufman: I'm pleased to inform you that your manuscript has been deemed suitable for publication in PLOS ONE. Congratulations! Your manuscript is now with our production department. If your institution or institutions have a press office, please let them know about your upcoming paper now to help maximize its impact. If they'll be preparing press materials, please inform our press team within the next 48 hours. 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. If we can help with anything else, please email us at plosone@plos.org. Thank you for submitting your work to PLOS ONE and supporting open access. Kind regards, PLOS ONE Editorial Office Staff on behalf of Dr. Catarina Leite Amorim Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0284256.r004

Open letter on the publication of peer review reports

PLOS recognizes the benefits of transparency in the peer review process. Therefore, we enable the publication of all of the content of peer review and author responses alongside final, published articles. Reviewers remain anonymous, unless they choose to reveal their names.

We encourage other journals to join us in this initiative. We hope that our action inspires the community, including researchers, research funders, and research institutions, to recognize the benefits of published peer review reports for all parts of the research system.

Learn more at ASAPbio .