Constitutive polysaccharide degradation and diet-dependent lipid metabolism reveal an adaptive feeding strategy in the pacific oyster Magallana gigas

Manabu W.L. Tanimura; Kazuhiko Koike; Kazumi Matsuoka

doi:10.1371/journal.pone.0347644

Peer Review History

Original SubmissionNovember 13, 2025
5 Mar 2026 Decision Letter - Mohammad Moniruzzaman, Editor -->PONE-D-25-61177-->-->Constitutive Polysaccharide Degradation and Diet-Dependent Lipid Metabolism Reveal an Adaptive Feeding Strategy in the Pacific Oyster Magallana gigas-->-->PLOS One Dear Dr. TANIMURA, 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 Apr 19 2026 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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Reviewer #2: Dear Authors, In this study, it is noteworthy that the transcriptomic responses of Magallana gigas related to polysaccharide degradation and lipid metabolism were examined under two different dietary conditions (terrestrial leaves and diatoms). The hypotheses that cellulase and hemicellulase enzymes may be constitutively expressed, while lipid and β-oxidation pathways may be regulated depending on diet composition, were tested. In my opinion, the hypothesis is meaningful from both ecological and metabolic perspectives. The experimental design directly aims to test this assumption. In this respect, the study presents a conceptually strong and coherent framework. The sequencing depth appears balanced between groups (approximately 34–39 million reads per sample, similar %GC values, and no low-quality sequences). The transcriptome assembly quality (BUSCO 92% complete) is at an acceptable level. Performing contamination control through genome alignment is also a positive methodological approach. The clear up-regulation of enzymes related to β-oxidation in the diatom group is biologically consistent and represents the strongest finding of the study. However, I suggest some minor improvements: Adding a PCA plot to show the distribution of replicates would be helpful. The model formula used in the DESeq2 analysis should be clearly stated. It should be clarified whether p-values were adjusted using FDR correction. Briefly mentioning dispersion values would increase statistical reliability. Regarding diet composition, the cellulose group received 0.5 g dry leaf, while the diatom group received 50 mL (1 × 10⁶ cells mL⁻¹). These two diets do not appear to be equivalent in terms of energy and nutrient content. Therefore, the comparison may reflect not only a “carbon type difference” but also a “nutritional quality difference.” This point is particularly important when interpreting lipase regulation. A short evaluation of the nutritional content of the diets and acknowledgment that the cellulose group may represent a lower-quality diet scenario would make the interpretation more balanced. It is known that bivalves can perform long-term metabolic suppression. Therefore, it may be briefly discussed whether one week of starvation is sufficient to induce a strong transcriptional response. The absence of pectinase detection is noteworthy. Since terrestrial leaf tissues may contain pectin, this point could be briefly discussed in the context of the literature, if possible. Consistency should be ensured in the use of p < 0.01 and p < 0.05 throughout the text. In addition, some figures in the manuscript file have low resolution. Especially under the heading “Regulated metabolic pathways,” part of the table is not clearly readable. Improving figure and table resolution would enhance the presentation quality. I find the findings related to lipid metabolism particularly convincing. With the clarifications and minor revisions mentioned above, I believe the study is suitable for publication. Sincerely, Referee ****** -->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 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? 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Revision 1
26 Mar 2026 Author Response Editor: All additional requirements from the editor have been addressed. Reviewer #1: The manuscript reports the findings of an original research work. The hypothesis was clearly stated and the experiment was conducted logically. The findings are interesting and the limitations of the study are well-stated for guiding the next step. The conclusions are made based on the evidence. ANS: We sincerely appreciate the reviewer’s comments and are pleased that the reviewer agrees with the content of this manuscript. Reviewer #2: Dear Authors, In this study, it is noteworthy that the transcriptomic responses of Magallana gigas related to polysaccharide degradation and lipid metabolism were examined under two different dietary conditions (terrestrial leaves and diatoms). The hypotheses that cellulase and hemicellulase enzymes may be constitutively expressed, while lipid and β-oxidation pathways may be regulated depending on diet composition, were tested. In my opinion, the hypothesis is meaningful from both ecological and metabolic perspectives. The experimental design directly aims to test this assumption. In this respect, the study presents a conceptually strong and coherent framework. The sequencing depth appears balanced between groups (approximately 34–39 million reads per sample, similar %GC values, and no low-quality sequences). The transcriptome assembly quality (BUSCO 92% complete) is at an acceptable level. Performing contamination control through genome alignment is also a positive methodological approach. The clear up-regulation of enzymes related to β-oxidation in the diatom group is biologically consistent and represents the strongest finding of the study. However, I suggest some minor improvements: Adding a PCA plot to show the distribution of replicates would be helpful. ANS: Thank you very much for this valuable suggestion. As this study primarily focuses on enzymes related to polysaccharide hydrolysis and lipid catabolism, we did not initially consider PCA as part of our analytical approach. However, upon performing PCA, we obtained interesting and informative results. As shown in Fig. 2, M. gigas appears to exhibit a consistent metabolic response when fed with diatoms, as the three replicates of the diatom-fed group cluster closely together. In contrast, the replicates from the reed leaf–fed group are more dispersed, suggesting greater variability in metabolic responses at the individual level. This pattern may indicate that M. gigas adopts multiple metabolic strategies, or simply becomes somewhat uncertain and tries various responses to cope with this low-nutrient diet environment. Although this does not constitute direct evidence, it makes sense to us in light of the idea that substrates that are ubiquitously available in the environment (e.g., terrestrial polysaccharides) may not trigger substantial metabolic adjustments. The model formula used in the DESeq2 analysis should be clearly stated. ANS: the model version of DESeq2 has been clearly stated. It should be clarified whether p-values were adjusted using FDR correction. ANS: In the present study, p-values were not initially adjusted using FDR correction. We recognize the potential risk of false positives and therefore performed an additional analysis with FDR correction (desired false discovery rate = 20%) for confirmation. After FDR correction, one cellulase-related transcript remained significant (being “discovery”), one xylanase-related transcript was no longer significant, the number of significant lipase-related transcripts decreased from 17 to 3, and the number of significant β-oxidation–related transcripts decreased from 29 to 4. Importantly, these changes did not alter the overall interpretation of the study. The purpose of this work is to explore general metabolic response patterns rather than to define a strict list of significantly regulated transcripts. In addition, given the relatively small number of biological replicates, FDR correction may be overly conservative and may mask biologically meaningful trends. For these reasons, we chose not to replace the original figures with the FDR-corrected version, but instead to clarify this point and report the FDR-corrected results in the main text. Briefly mentioning dispersion values would increase statistical reliability. ANS: We thank the reviewer for this helpful suggestion. The analysis was conducted using our in-house-built R script, which incorporated functions from the DESeq2 package for differential expression modeling and dispersion estimation, and this has now been briefly described in the revised manuscript. As shown in the dispersion plot, the fitted dispersion values exhibit a smooth mean–dispersion trend, and the final dispersion estimates (blue dots) follow this trend quite closely. Regarding diet composition, the cellulose group received 0.5 g dry leaf, while the diatom group received 50 mL (1 × 10⁶ cells mL⁻¹). These two diets do not appear to be equivalent in terms of energy and nutrient content. Therefore, the comparison may reflect not only a “carbon type difference” but also a “nutritional quality difference.” This point is particularly important when interpreting lipase regulation. A short evaluation of the nutritional content of the diets and acknowledgment that the cellulose group may represent a lower-quality diet scenario would make the interpretation more balanced. ANS: We thank the reviewer for this important comment. We agree that the two feeding treatments were not nutritionally equivalent and that the observed differences may reflect not only carbon source type, but also differences in overall nutritional quality and energy availability. We have now clarified this point in the revised manuscript and discussed the possibility that the transcriptomic responses observed in the reed leaf–fed group, particularly those related to lipid metabolism, may reflect not only substrate preference but also a low-nutrient or near-starvation physiological state. It is known that bivalves can perform long-term metabolic suppression. Therefore, it may be briefly discussed whether one week of starvation is sufficient to induce a strong transcriptional response. ANS: We agree that one week of starvation may not necessarily be sufficient to induce the full transcriptional response associated with severe nutrient deprivation. We have now added discussion in the revised manuscript to acknowledge that the transcriptomic changes observed in the present study may represent responses to an intermediate or partial starvation state rather than to complete metabolic suppression. This may also help explain the variability observed in the reed leaf–fed group. We agree that future studies comparing multiple starvation durations would be valuable for better understanding the timing and extent of transcriptional responses in M. gigas under different dietary conditions. The absence of pectinase detection is noteworthy. Since terrestrial leaf tissues may contain pectin, this point could be briefly discussed in the context of the literature, if possible. ANS: We are glad that the reviewer found this point interesting. We also found it both surprising and intriguing that M. gigas does not appear to possess any pectinase-related genes. One possible explanation is that pectin degradation may not provide sufficient nutritional advantage for M. gigas, especially when compared with other substrates such as proteins, lipids, or even cellulose. Another possibility is that pectin may not be sufficiently abundant in the oyster’s natural environment to favor the retention of such genes through evolution. We have now added a paragraph discussing these possibilities in the revised manuscript. Consistency should be ensured in the use of p < 0.01 and p < 0.05 throughout the text. ANS: Thank you for this comment. The p-value thresholds have now been revised to ensure consistency throughout the manuscript (the set of transcripts used for the KAAS search was reanalyzed and revised accordingly). This modification did not alter any of the conclusions or results presented in the paper, as this step was used only for the extraction of potentially differentially expressed pathways. In addition, some figures in the manuscript file have low resolution. Especially under the heading “Regulated metabolic pathways,” part of the table is not clearly readable. Improving figure and table resolution would enhance the presentation quality. ANS: High-resolution versions of the figures and tables will be provided in the revised manuscript to improve clarity and presentation quality. I find the findings related to lipid metabolism particularly convincing. With the clarifications and minor revisions mentioned above, I believe the study is suitable for publication. Sincerely, Referee Attachments Attachment Submitted filename: Answers to the reviewers.pdf https://doi.org/10.1371/journal.pone.0347644.r002
6 Apr 2026 Decision Letter - Mohammad Moniruzzaman, Editor <p>Constitutive Polysaccharide Degradation and Diet-Dependent Lipid Metabolism Reveal an Adaptive Feeding Strategy in the Pacific Oyster Magallana gigas PONE-D-25-61177R1 Dear Dr. TANIMURA, 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. For questions related to billing, please contact and clicking the ‘Update My Information' link at the top of the page. For questions related to billing, please contact billing support.. 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, Mohammad Moniruzzaman Academic Editor PLOS One ********** https://doi.org/10.1371/journal.pone.0347644.r003
Formally Accepted
Acceptance Letter - Mohammad Moniruzzaman, Editor PONE-D-25-61177R1 PLOS One Dear Dr. TANIMURA, 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. You will receive an invoice from PLOS for your publication fee after your manuscript has reached the completed accept phase. If you receive an email requesting payment before acceptance or for any other service, this may be a phishing scheme. Learn how to identify phishing emails and protect your accounts at https://explore.plos.org/phishing. 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 Dr. Mohammad Moniruzzaman Academic Editor PLOS One https://doi.org/10.1371/journal.pone.0347644.r004

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