Histological and molecular characterization of the digestive system of early weaned juveniles of Arapaima sp. reared in a recirculating aquaculture system

Maria J. Darias; Guillain Estivals; Karl B. Andree; Christian Fernández-Méndez; Roger Bazán; Chantal Cahu; Enric Gisbert; Diana Castro-Ruiz

doi:10.1371/journal.pone.0323012

Peer Review History

Original SubmissionSeptember 28, 2024
28 Sep 2024 Author Response https://doi.org/10.1371/journal.pone.0323012.r001
5 Nov 2024 Decision Letter - Mohammed Fouad El Basuini, Editor -->PONE-D-24-43490-->-->Histological and molecular characterization of the digestive system of early weaned juveniles of Arapaima sp. reared in a recirculating aquaculture system-->-->PLOS ONE Dear Dr. Darias, 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 Dec 20 2024 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. 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(Please upload your review as an attachment if it exceeds 20,000 characters)--> Reviewer #1: There are no recommendations The most descriptive methodologies are without any references --why/how There are no declaration of conflict interests There are no authors contributions There are no data availability There is no ethical approval statement Materials and methods very long and repeated --for example---LN/173---after the authors mentioned the histological analysis back to write it and start to mention again There are no reference for the statistical analysis ? LN/258--write as statistical analysis not else with an updated references Results and discussion --going to be chapter like Abstract: There are no highlights There are no graphical abstract The keywords should be written after the abstract not before LN/24-25--clarify the differences between the monotypic genus and multiple species LN/26---tendencies---detailed this LN/33-36--more details are requested There are many things related to the introduction and materials and methods ---should not included at the abstract Divide the abstract into backgrounds-aims/methods/results and conclusion Add carnivores /aquaculture industry / food quality , histology and molecular analysis to the keywords Introduction: LN/50---determine the time to reach LN/51--why R is capital with river LN/58---what is this ? LN/59-60---2 different style in writing the references Introduction is extremely very long , repeated without any need Aims need to be more clarified Novelty of this study should be more highlighted Materials and methods LN/64--write as materials and methods not VS LN/66--prepared--means what and add reference LN/69-87---add reference LN/73---why empty LN/88-98--also without any references LN/99-106--add reference The authors did not mention any thing about the statistical analysis Materials and methods : What about the IACUC code --should be enclosed LN/115-123---add reference LN/124--write as a separate item ---experimental design How many fishes did you use/groups LN/135-143----very long --no need LN/155---you should also write as a separate items--as histological analysis Regarding the histological analysis ---complete details about the paraffin embedding technique should be enclosed with an updated references Results : Huge number of abbreviations were used---tabulate all as general Write as Table(1):---------/Fig.(1):----etc--apply for all There are no figure descriptions Results --- Is very long What about the clinical signs of the treated fishes What about the PM changes What about the percentage of mortalities--if there is Resulst and discussion --going to be chapter like Discussion : Rewrite it again Conclusion : Less than enough References: Some cited references need to be more update Huge number of references were used (102)??? There are no plan for the study area ? Reviewer #2: Comments to the Authors I have reviewed your manuscript titled "Histological and molecular characterization of the digestive system of early weaned juveniles of Arapaima sp. reared in a recirculating aquaculture system" and would like to offer constructive feedback. I appreciate your effort and dedication and look forward to helping you enhance the quality of your work. Below, I will outline several points that require further consideration and improvement. 1. Abstract, Lines 23-29: Please delete or summarize the background information and proceed directly to the aim of the study. 2. Abstract, Lines 30-35: Please merge the aim of the study to avoid repetition. 3. Abstract: Please include specific recommendations in the conclusion to enhance clarity. 4. Abstract: In conclusion, please discuss your results and suggest directions for future studies. 5. Could you please provide the keywords for this study? 6. Introduction, Lines 96-112: The introduction is overly lengthy, and the aim is expressed in too many words. Please revise to clearly emphasize the aim of the study. 7. Lines 129 and Table 1: The value of crude lipid differs between the text and Table 1. Please verify and correct this discrepancy. 8. Did you use any anesthetics in the experiment? 9. Table 1: All full names of abbreviations, such as gene names, MUST be defined in the footnotes. 10. Line 261: Please italicize “(P < 0.05)”. Additionally, check the entire manuscript for consistent formatting. 11. I have noticed a few minor errors and spelling mistakes scattered throughout the manuscript. To enhance the linguistic quality of the manuscript, I would recommend considering professional language revision. ****** -->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. 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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: Comments to Authors PONE-D-24-43490.doc https://doi.org/10.1371/journal.pone.0323012.r002
Revision 1
30 Mar 2025 Author Response Replies to reviewer comments We sincerely appreciate the time and effort of both reviewers in evaluation our manuscript. Their constructive feedback has helped us improve the clarity and quality of our study. Below, we provide detailed responses to each comment and outline the revisions made in the manuscript accordingly. Reviewer #1: There are no recommendations The most descriptive methodologies are without any references --why/how Response: We have added additional references where necessary to support the methodological descriptions. However, some methods are widely used, while others follow manufacture’s protocols (e.g., molecular biology techniques), which do not usually require specific citations. There are no declaration of conflict interests Response: We are unsure which information is visible to the reviewers, but a competing interests’ statement was provided during submission, following the instructions of the journal. The authors have declared that no competing interests exist. There are no authors contributions Response: Author contributions were also included in the online submission in accordance with journal guidelines. There are no data availability Response: The required data availability statement was also provided during submission, indicating that all relevant data are included within the manuscript and its Supporting Information files. There is no ethical approval statement Response: This information was included in the original manuscript (L168-171; L146-149 in the revised version) and provided online during submission. At the time of the study, no local ethical committee existed at the IIAP in Iquitos, Peru, the country’s main Amazonian aquaculture research institution. However, as part of a Peruvian-French-Spanish collaboration, all animal procedures adhered to the European Union Council guidelines (2010/63/EU). Compliance was ensured by the lead author, who is certified in animal experimentation by the French Ministry of Agriculture and Fisheries. Materials and methods very long and repeated --for example---LN/173---after the authors mentioned the histological analysis back to write it and start to mention again Response: We reviewed and reorganized the manuscript to eliminate unintended repetition. The “Sampling and growth measurements” section originally described sample preservation methods for the subsequent histological and gene expression analyses (LL155-160 of the original submission), while the “Histological analyses” section detailed the specific analytical techniques. However, we have revised these sections for improved clarity. There are no reference for the statistical analysis? Response: We have added a reference. LN/258—write as statistical analysis not else with an updated references Response: The section title has been updated to “Statistical analyses,” as suggested. Results and discussion --going to be chapter like Response: The meaning of this comment is unclear. However, we have carefully revised both sections and have also shorten the discussion considerably. Abstract: There are no highlights Response: PLOS ONE guidelines do not require highlights. There are no graphical abstract Response: Similarly, PLOS ONE guidelines do not request a graphical abstract. The keywords should be written after the abstract not before Response: Keywords were provided during submission and not in the manuscript, as per journal requirements. Their placement in the reviewer’s version may depend on how the submission system displays them. LN/24-25--clarify the differences between the monotypic genus and multiple species Response: A monotypic genus contains a single species, unlike other genera that contain multiple species. This is standard terminology that typically does not require further explanation. LN/26---tendencies---detailed this Response: This tendency refers to plant ingestion. However, this information is no longer present in the revised abstract. LN/33-36--more details are requested Response: We revised the abstract to include additional detail within the 300-word limit. There are many things related to the introduction and materials and methods ---should not included at the abstract Response: The abstract has been revised based on the reviewer’s feedback. Divide the abstract into backgrounds-aims/methods/results and conclusion Response: PLOS ONE guidelines (PLOS ONE style templates) do not require sectioned abstracts. We have structured the abstract according to their format: “The Abstract should: i) Describe the main objective(s) of the study; ii) Explain how the study was done, including any model organisms used, without methodological detail; iii) Summarize the most important results and their significance; iv) Not exceed 300 words.” Add carnivores /aquaculture industry / food quality , histology and molecular analysis to the keywords Response: It is generally recommended that keywords avoid duplicating words already used in the title. Therefore, we don’t believe that “histology and molecular analysis” should be added to the keywords. We have replaced “early weaning” with “Peruvian aquaculture”, to align with the reviewer’s recommendation (aquaculture industry) while maintaining a geographical focus. For the rest, we opted to retain our original keywords, as they accurately reflect the study’s focus and complement the title, such as “paiche” (common name of the species in Peru), “Amazon basin” (natural habitat), “digestive gene expression,” and “ontogeny.” Furthermore, this paper does not focus on “carnivores” (we are actually showing that our species has characteristics of an omnivorous species) or “food quality”. Introduction: LN/50---determine the time to reach Response: These values are historical maximums observed in nature, which are less frequently observed today due to overfishing. The time necessary to achieve them is not well-documented, although it is thought to be between 4 and 7 years. However, we prefer not to include this information as it is not well-supported. Many papers on Arapaima spp. mention these historical data in a similar way to us. LN/51--why R is capital with river Response: “Essequibo River” is often capitalized as a formal name, but we have changed it to lowercase. LN/58---what is this ? Response: We have defined CITES as the Convention on International Trade in Endangered Species of Wild Fauna and Flora. LN/59-60---2 different style in writing the references Response: Schinz 1822 is a species authority notation, not a reference. Parentheses indicate reclassification under a different genus than originally described. Introduction is extremely very long , repeated without any need Response: The introduction has been streamlined to improve clarity and conciseness. Aims need to be more clarified Response: The aims have been reformulated to address the comments of both reviewers. The second reviewer requested a more synthesized description of the aims. Novelty of this study should be more highlighted Response: We have emphasized the study’s novelty in the introduction. Materials and methods Overall comment: The line numbers indicated by the reviewer in the next six comments do not correspond to the lines of the Material and Methods section. Where possible, we have identified and addressed the comments accordingly. LN/64--write as materials and methods not VS Response: We were unable to identify what this refers to. LN/66--prepared--means what and add reference Response: The term “prepared” is only used once in the paper in the L 176 of the original submission (“Paraffin blocks were prepared in an AP280-2Myr station”). We are not sure what the reviewer requires. Paraffin blocks are prepared by embedding the samples in paraffin, as described in the previous sentence. This is a standard procedure in sample preparation for histological analysis. The reference “Sarasquete and Gutiérrez, 2005”, which was inadvertently not formatted correctly, was already included and we have added an additional one. LN/69-87---add reference Response: If the previous comment regarding L 66 actually refers to L 176 in the initial submitted version, we assume that the reviewer may be referring to LL 179-197. If that is the case, we have added a reference in LL 159 and 174 to complement those that were already included in LL 162, 164, and 177. LN/73---why empty Response: We could not locate the term “empty” in the manuscript. LN/88-98--also without any references Response: If the reviewer refers to the “Partial mRNA amplification and identification” section, we have added reference (LL 198 and 206). However, we would like to highlight that, as mentioned in LL 184, 188, and 197, this section often follows manufacture’s protocols. LN/99-106--add reference Response: If the reviewer refers to the “Partial mRNA amplifcation and identification” section, references have been included in LL 227 and 233. The authors did not mention any thing about the statistical analysis Response: We are not sure what the reviewer refers to. The statistical analyses were described in the original LL 258-263. However, we have made several modifications (LL 242-249). Materials and methods : What about the IACUC code --should be enclosed Response: As previously mentioned, animal experimental procedures are documented in LL146-149 and were also included in the submission process. LN/115-123---add reference Response: We have added relevant references in L 104 regarding the taxonomic uncertainties (which were already provided in the introduction). However, for the rest of the text, we cannot add references as it refers to our specific rearing conditions. LN/124--write as a separate item ---experimental design Response: Given that the description of our experimental design is concise, we believe presenting the information in a single subsection is more appropriate. How many fishes did you use/groups Response: The manuscript provides details on fish density and the water volume per tank. Specifically, 1 ind L-1 in 30 L = 30 fish per tank (LL 106-108). LN/135-143----very long --no need Response: Diet composition details are essential in aquaculture nutrition for reproducibility and comparisons with similar studies. Therefore, we cannot remove this information. LN/155---you should also write as a separate items--as histological analysis Response: We have integrated this text into the histological analysis section (LL 152-177), although it referred to sample preservation during experimentation rather than the analytical methods themselves. Regarding the histological analysis ---complete details about the paraffin embedding technique should be enclosed with an updated references Response: We have added some additional details; however, paraffin embedding is a very standard procedure that typically does not require further details or updated references. Results : Huge number of abbreviations were used---tabulate all as general Response: The only abbreviations used in the main text of the results are TL (total length) and WW (wet weight), which are defined upon their first mention in the Introduction and Material and Methods sections, respectively (L 60 and L136), as well as gene name abbreviations, which have also been defined previously. It seems the reviewer may be confusing the figure captions appearing directly after the paragraph in which they are first cited (see comments below), where each abbreviation is defined in the respective figure caption. Write as Table(1):---------/Fig.(1):----etc--apply for all Response: We followed the guidelines mentioned in the PLOS ONE style templates (PLOSOne_formatting_sample_main_body.pdf), which specify citing figures as “Fig 1”, “Fig 2”, etc., and tables as “Table 1”, “Table 2”, etc. There are no figure descriptions Response: In accordance with PLOS ONE guidelines, the captions for the 12 figures appear directly after the paragraph in which they are first cited. It seems the reviewer may have mistaken them as part of the main text. Each of the paragraphs starting with Fig X. correspond to a figure caption: Fig 1: LL 261-265 Fig 2: LL 275-280 Fig 3: LL 299-306 Fig 4: LL 308-316 Fig 5: LL 339-352 Fig 6: LL 378-396 Fig 7: LL 398-407 Fig 8: LL 459-468 Fig 9: LL 470-483 Fig 10: LL 506-512 Fig 11: LL 538-543 Fig 12: LL 561-565 Results --- Is very long Response: The level of detail in the main text is standard for studies describing the histology of the digestive system in fish species. However, since the reviewer may not have recognized the presence of figure captions, they might be assessing the results section as a single text block, including both the main text and figure captions. These captions are positioned throughout the results section after each relevant paragraph (see lines above), in accordance with the journal’s guidelines. Nearly 40% of the section consists of captions for the 12 figures, so the main text of the results section is considerably shorter than what the reviewer may have perceived. What about the clinical signs of the treated fishes Response: This is a classical nutritional study with a single diet and, as such, it did not involve fish treatments. Clinical signs were not a relevant variable. What about the PM changes Response: If “PM” refers to postmortem changes, these were not part of our study’s scope nor relevant to its conclusions. What about the percentage of mortalities–if there is Response: The survival rate is provided in L 259, from which the mortality rate can be easily inferred. Resulst and discussion –going to be chapter like Response: The discussion section has been rewritten to improve clarity and conciseness. Discussion : Rewrite it again Response: The discussion section has been revised to reduce its length and improve the flow and clarity. Conclusion : Less than enough Response: The conclusion sections has been expanded to provide a clearer summary of the findings. References: Some cited references need to be more update Response: Older references are cited to credit foundational studies. We have reviewed all citations to confirm accuracy and relevance. Huge number of references were used (102)??? Response: The number of references reflects the detail of our study, aligning with PLOS ONE’s policy to include any relevant works. However, the number of references has been reduced to 77 after rewriting the discussion section. There are no plan for the study area ? Response: Since this is a controlled experiment in an indoor recirculating aquaculture system located in a research institute, there is no geographic study area to map. Instead, the location is provided in the Materials and Methods section in LL 102-103. Reviewer #2: Comments to the Authors I have reviewed your manuscript titled "Histological and molecular characterization of the digestive system of early weaned juveniles of Arapaima sp. reared in a recirculating aquaculture system" and would like to offer constructive feedback. I appreciate your effort and dedication and look forward to helping you enhance the quality of your work. Below, I will outline several points that require further consideration and improvement. 1. Abstract, Lines 23-29: Please delete or summarize the background information and proceed directly to the aim of the study. Response: We have revised the abstract following the reviewer’s comments. 2. Abstract, Lines 30-35: Please merge the aim of the study to avoid repetition. Response: Done 3. Abstract: Please include specific recommendations in the conclusion to enhance clarity. Response: Done. Thank you for this suggestion. 4. Abstract: In conclusion, please discuss your results and suggest directions for future studies. Response: Done. Thank you for this suggestion. 5. Could you please provide the keywords for this study? Response: Keywords were provided during the original submission and not included in the manuscript, as per journal requirements. Reviewer #1 commented on the keywords, so we understand that they are visible to the reviewers. The keywords are: Paiche; Amazon basin; Peruvian aquaculture; digestive gene expres Attachments Attachment Submitted filename: Response to Reviewers.docx https://doi.org/10.1371/journal.pone.0323012.r003
1 Apr 2025 Decision Letter - Mohammed Fouad El Basuini, Editor Histological and molecular characterization of the digestive system of early weaned juveniles of Arapaima sp. reared in a recirculating aquaculture system PONE-D-24-43490R1 Dear Dr. Darias, 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 will be generated when your article is formally accepted. Please note, if your institution has a publishing partnership with PLOS and your article meets the relevant criteria, all or part of your publication costs will be covered. Please make sure your user information is up-to-date by logging into Editorial Manager at Editorial Manager® and clicking the ‘Update My Information' link at the top of the page. If you have any questions relating to publication charges, 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, Mohammed Fouad El Basuini, Professor Academic Editor PLOS ONE Additional Editor Comments (optional): Reviewers' comments: https://doi.org/10.1371/journal.pone.0323012.r004
Formally Accepted
Acceptance Letter - Mohammed Fouad El Basuini, Editor PONE-D-24-43490R1 PLOS ONE Dear Dr. Darias, I'm pleased to inform you that your manuscript has been deemed suitable for publication in PLOS ONE. Congratulations! Your manuscript is now being handed over to our production team. At this stage, our production department will prepare your paper for publication. This includes ensuring the following: * All references, tables, and figures are properly cited * All relevant supporting information is included in the manuscript submission, * There are no issues that prevent the paper from being properly typeset You will receive further instructions from the production team, including instructions on how to review your proof when it is ready. Please keep in mind that we are working through a large volume of accepted articles, so please give us a few days to review your paper and let you know the next and final steps. Lastly, 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 customercare@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. Mohammed Fouad El Basuini Academic Editor PLOS ONE https://doi.org/10.1371/journal.pone.0323012.r005

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