Peer Review History
Original SubmissionFebruary 26, 2021 |
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PONE-D-21-06556 Microbial assemblages and methanogenesis pathways impact on methane production and foaming in manure deep-pit storages PLOS ONE Dear Dr. Yang, 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. Please submit your revised manuscript by May 24 2021 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:
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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: Yes Reviewer #3: Yes ********** 2. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes Reviewer #2: Yes Reviewer #3: Yes ********** 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: No Reviewer #2: Yes Reviewer #3: 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 Reviewer #3: 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 authors compared physical and chemical properties of different types of swine manure pit samples (no-foam, foam, and crust), and made associations of these with the bacterial and methanogen community structure, and methane production rate. The work is interesting and generally well-performed, and it does shed light on some of the differences in these sample types. Despite these advances, the reviewer feels that the authors could have extended their observations by delving a bit more into the characteristics of the samples, particularly with regard to the SCFA and LCFA (see Specific comments below), as both types of compounds are major substrates or intermediates and their metabolic fates have a strong influence on methane production and, presumably, microbial community structure. A second issue regards the pH of the samples, and how it might relate to SCFA concentration and to methane production. It appears from L66 and Supplemental Figure S3 that pH was measured, and there was a slight correlation of pH with some of the other measured characteristics (particularly nutrients), especially in the no-foam manures, but little correlation of pH with SCFA. This should perhaps be pointed out somewhere in the text. It would also be useful to indicate the range of pH values encountered, and whether they differed significantly among the manure types. As the aceticlastic methanogens tend to be more sensitive to acidic conditions than are the hydrogenotrophic methanogens, could pH explain the general absence of the former group in these samples? Specific comments: L50: The authors bring up the tendency of foaming to cause a potential for explosion, but in the Results we learn that the foaming samples showed lower rates of methane production than did the other samples. Presumably the foaming causes methane accumulation even if it is produced in lesser amounts. This should be mentioned in the Discussion. L64-67: The methods description is inadequate. Reference 4 does not provide analytical methods, and no methods are described for LCFA and SCFA analysis. L115, L126: How were these sequence numbers (10k for bacteria, 4k for methanogens) selected, as opposed to normalizing the number of reads selected to number of reads in the sample with the fewest reads? L158-161: It would be very useful to be more specific regarding these sample types, perhaps by including photographs (even if included in Supplementary data). L181-183: Another important difference between SBM and DDGS is the amount and type of LCFAs, which should have some bearing in discussion of the importance of LCFA and its metabolism in the three sample types. L209-211: This seems like a superficial distinction, as the “physical interactions” must have some sort of underlying chemical basis (e.g., surface tension is probably governed by the relative contributions and hydrophobic/hydrophilic behavior of proteins, lipids and polysaccharides). L228-254: In this section the authors discuss SCFA and acetic acid in the samples without providing any data on the amounts and distributions (i.e., different chain lengths) of these acids. Such information would be very useful in interpreting potential bottlenecks in LCFA degradation to SCFA, and SCFA catabolism to methane. L256: This is an oversimplification. Perhaps the authors should add “under standard conditions”. The process of LCFA degradation to SCFA typically operates near equilibrium, so that it is quite sensitive to the relative concentrations of substrate and product. But it does not typically require input of energy, and the authors seem to suggest this in the following sentences, in which they state that methanogenesis provides thermodynamic displacement via H2 consumption, allowing SCFA catabolism to occur. L320-321: It is not clear to the reviewer how the individual slope values for the three types of manures can be compared to yield statistically significant differences, as there is only a single slope value for each sample type.. L349-360: These are interesting observations, but they raise the question of where the acetic acid goes. Working back to comments to L228-254 above, is it possible that some members of the bacterial community might be engaged in chain elongation reactions, in which acetate is converted to longer SCFA such as butyrate and caproate? Chain elongation has been widely observed in waste pits and anaerobic reactors in which aceticlastic methanogenesis is limited (for example, see Zhu et al., DOI: 10.1038/srep14360, or Angenent et al., DOI: 10.1021/acs.est.5b04847). L398-401: What is meant here by the vague statement regarding “the different potential involvement of bacteria or methanogens”? L421-424: The reviewer is not convinced by this statement. Why can’t the accumulation of SCFA be due to impaired catabolism of SCFA, rather than invoking a greater production of SCFA from other feed components? Table S2: Please define (in a footnote) the term “integrator”. Minor edits: L45-46: Delete “However,” and use rest of sentence as the first sentence of the next paragraph. L50: Delete “conditions of”. L185: Change “low” to “poorly”. L229: Here and elsewhere in the manuscript, change “SCFA/acetic acid” to just “SCFA”, because (as pointed out in L233-234) acetic acid is one of the SCFA. L277: Change “between” to “among”. L329: Change “genera” to “genus”. L347: Change “that the bacterial or methanogen groups were the most abundant in” to “in which the bacterial or methanogen groups were the most abundant”. Reviewer #2: Manuscript entitled "Microbial assemblages and methanogenesis pathways impact on methane production and foaming in manure deep-pit storages" can be considered as high importance. This manuscript provides relatively new and unique dataset to tackle the human, animal and environmental risks associated with swine industry. The study provided a relatively large dataset to support the finding. Manuscript is well written and deserve publications. Few things, however, authors are suggested to consider: 1) provide the details of farm (herd size; pit size; and existing manure management in farms where samples were collected); 2) Figure 1 requires further descriptions in Figure captions (currently not clear); 3) method section requires further clarifications improvement in terms of sampling protocol, and the strategies implemented in sample collection; 4) before ending results and discussion section, authors are suggested to provide major findings quantitatively, and limitations of the study; and 5) discussion on the composition of gas formation, ammonia, and microbial community identified in Figure 5,6.7. Any pathogens, in addition to methanogens were identified? Further, in statistics table, authors are suggested to provide the sample numbers used for the analysis. In terms of feed characterization, not sure if the feed of individual farms has been characterized or the feed from mills which supplies the feed has been characterized. Each pit will have certain holding capacity, and the retention time will be having impacts of microbial community. Therefore, the conditions of pits (mixing, retention time, temperature, flushing frequency, and the frequencies of disloading of those pits are important consideration while describing the shift in microbial community under anaerobic conditions. Reviewer #3: This manuscripts describes the bacterial and methanogenic communities of manure collected from 46 swine farms at several different time points. The authors visually classified the manure surface as either non-foaming, crust-forming or foaming at each sampling time. Certain chemical properties of the manure were also assessed. The authors report that the swine diet influences the manure surface texture and that certain chemical and physical properties were correlated with the manure surface texture as well. The non-foaming and foaming manure bacterial and methanogenic microbial communities were most dissimilar from each other. Major comments The materials and methods for the manure sampling and chemical analysis appear to be missing. The superscript “4” is included at the end of the sentence on ln 65 but it is unclear if this is referring to REF 4 or something else. Minor comments In Table S2 should the P-values for Farm and Feed Mill for bacteria also be 0.001? Can the x-axis in Fig. 5 C and D be converted to percent relative abundance rather than the current scale which is not very intuitive. Ln 24: “an increased” Ln 26-27: “…rRNA and archaeal mcrA genes…” Ln 29: “and that the bacterial…” Ln 31: “previously” should be removed since they are still uncharacterized. Ln 33, 362: “relative abundance” Ln 50: I would remove “conditions of” Ln 81: “mcrA gene was” Ln 111-113: What database was used for 16S rRNA gene classification? Ln 121: “chimeras” Ln 180: What is meant by “more significant” here? A greater concentration of DDGS? Also, what does the superscript “19” refer to here? Ln 182: “NDF” should be first defined here rather than on ln 185. Ln 205, 407: “were correlated” Ln 228: The use of “SCFA/acetic acid” here and elsewhere is unclear to the review. Was acetic acid the only SCFA measured? Ln 275: Remove “occurrence of” Ln 338: “of shared and unique A) bacterial and B) methanogenic OTUs of no-foam…” Ln 340: “most relatively abundant” Ln 342: “that differed”; “are shown” Ln 346: “relatively abundant” Ln 361: “taxa” Ln 364: “was positively correlated”; “Bacilli (Lactobacillus) OTU and…” Ln 366: I would remove “members of” Ln 367-368: “…content was also negatively” Ln 371: “between individual bacterial taxa and” Ln 377: “…or bacterial and methanogenic groups at the class level” Ln 383, 393, 395: “were positively correlated” Ln 386: “unclassified Firmicutes OTU was also positively…” Ln 389: “suspect that the” Ln 390: Use “absence of” or “lack of” rather than “missing” here. Ln 397: “has previously been…” Ln 404: “is strongly correlated” Ln 407: Remove “observed” Ln 416: “observed that the” Ln 418: “as evidenced” Ln 424: “matter” Ln 429: “that there are” ********** 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: Yes: Pramod Pandey Reviewer #3: No 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. |
Revision 1 |
PONE-D-21-06556R1 Microbial assemblages and methanogenesis pathways impact on methane production and foaming in manure deep-pit storages PLOS ONE Dear Dr. Yang, 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. Please submit your revised manuscript by Jul 31 2021 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:
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: http://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, Alex V Chaves, 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. 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: (No Response) Reviewer #2: All comments have been addressed Reviewer #3: 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: Yes Reviewer #2: Yes Reviewer #3: Yes ********** 3. Has the statistical analysis been performed appropriately and rigorously? Reviewer #1: Yes Reviewer #2: Yes Reviewer #3: 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 Reviewer #3: 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 Reviewer #3: 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 adequately addressed the reviewers comments. One additional question arises: L386: This does not make sense to the reviewer. Hydrogenotrophic methanogens oxidize H2, and use the reducing equivalents to reduce CO2. How do they oxidize acetate? Minor edits: Title: Suggest deleting “on”. L43 and L62: Please use SI units (meters, rather than ft). L119, L131: Change “less” to “fewer”. L256: Change “microorganism metabolism” to “microbial metabolism”. L257: Change “many” to “most”. L279-281: This is a little confusing as written. Suggest changing “Under standard anaerobic conditions, the breakdown of LCFA is carried out via acetogenesis [35,42]. This process is energy-consuming and non-spontaneous.”, to “Under anaerobic conditions, the breakdown of LCFA is carried out via acetogenesis [35, 42]. This process is endergonic and does not occur spontaneously under standard conditions.” L298: Insert “, respectively” after “methanogens”. L458: Change “fibers” to “fiber”. Reviewer #2: Authors revised manuscript, and revised version of manuscripts responded answers to comments line by line, and issues raised have been resolved. Reviewer #3: (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: Yes: Pramod Pandey Reviewer #3: No 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. |
Revision 2 |
Microbial assemblages and methanogenesis pathways impact methane production and foaming in manure deep-pit storages PONE-D-21-06556R2 Dear Dr. Yang, 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, Alex V Chaves, PhD Academic Editor PLOS ONE |
Formally Accepted |
PONE-D-21-06556R2 Microbial assemblages and methanogenesis pathways impact methane production and foaming in manure deep-pit storages Dear Dr. Yang: 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 Prof Alex V Chaves Academic Editor PLOS ONE |
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