Molecular Advances and Sustainable Strategies in Mushroom Production for Food Security: A Review
Round 1
Reviewer 1 Report
This article is a comprehensive review that examines the role of mushroom production in the context of sustainability and food security, within the framework of bibliometric analysis, ecological adaptations, and molecular approaches. The strengths of the study include a large-scale search of current literature, systematic bibliometric analysis based on the Web of Science database, and an emphasis on the integration of molecular biology into sustainable agriculture. However, the article generally remains descriptive and illustrative. It suffers from several fundamental shortcomings in terms of critical synthesis, methodological transparency, and a clear presentation of original contributions. In particular, the connection established between bibliometric analysis and advanced molecular approaches appears weak at both the conceptual and analytical levels.
Below are my detailed comments regarding the article:
1- The Web of Science search strategy (full search strings, fields: title/abstract/keywords), exclusion criteria, and how duplicate entries are handled are not clearly explained. Furthermore, although the decline for 2025 is explained by "indexing lag," this assumption is not methodologically supported.
2. Although keyword networks and MCA results are presented, the reasons why these results led to the selection of specific molecular approaches (transcriptomics, CRISPR, synthetic biology, etc.) are not sufficiently justified analytically. The bibliometric analysis remains largely descriptive.
3. Transcriptomic, proteomic, and genomic studies are listed; however, the concrete mechanistic contributions of these approaches to production efficiency, stress tolerance, or lignocellulose degradation are not discussed in depth. There is no comparative synthesis across studies.
4. Although the research gap in the Middle East and arid regions is highlighted, case studies, species-based adaptations, or specific environmental stressors (high temperature, salinity, water scarcity) from these regions are not sufficiently detailed.
5. Mycorrhizal relationships, microbiome integration, and molecular regulation are presented separately; however, a clear scheme or model in which these are combined under an integrated production model or conceptual framework is not proposed. 6- Studies are generally presented in their positive aspects, with contradictory findings, methodological limitations, or unsuccessful applications almost never discussed. This reduces the critical depth of the review.
7- The conclusion section is largely a repetition of the previous parts of the text. Concrete research priorities for the future, methodological recommendations, or policy-implementation implications are not presented in a clearer and more original way.
This article is a comprehensive review that examines the role of mushroom production in the context of sustainability and food security, within the framework of bibliometric analysis, ecological adaptations, and molecular approaches. The strengths of the study include a large-scale search of current literature, systematic bibliometric analysis based on the Web of Science database, and an emphasis on the integration of molecular biology into sustainable agriculture. However, the article generally remains descriptive and illustrative. It suffers from several fundamental shortcomings in terms of critical synthesis, methodological transparency, and a clear presentation of original contributions. In particular, the connection established between bibliometric analysis and advanced molecular approaches appears weak at both the conceptual and analytical levels.
Below are my detailed comments regarding the article:
1- The Web of Science search strategy (full search strings, fields: title/abstract/keywords), exclusion criteria, and how duplicate entries are handled are not clearly explained. Furthermore, although the decline for 2025 is explained by "indexing lag," this assumption is not methodologically supported.
2. Although keyword networks and MCA results are presented, the reasons why these results led to the selection of specific molecular approaches (transcriptomics, CRISPR, synthetic biology, etc.) are not sufficiently justified analytically. The bibliometric analysis remains largely descriptive.
3. Transcriptomic, proteomic, and genomic studies are listed; however, the concrete mechanistic contributions of these approaches to production efficiency, stress tolerance, or lignocellulose degradation are not discussed in depth. There is no comparative synthesis across studies.
4. Although the research gap in the Middle East and arid regions is highlighted, case studies, species-based adaptations, or specific environmental stressors (high temperature, salinity, water scarcity) from these regions are not sufficiently detailed.
5. Mycorrhizal relationships, microbiome integration, and molecular regulation are presented separately; however, a clear scheme or model in which these are combined under an integrated production model or conceptual framework is not proposed. 6- Studies are generally presented in their positive aspects, with contradictory findings, methodological limitations, or unsuccessful applications almost never discussed. This reduces the critical depth of the review.
7- The conclusion section is largely a repetition of the previous parts of the text. Concrete research priorities for the future, methodological recommendations, or policy-implementation implications are not presented in a clearer and more original way.
Author Response
We thank the reviewer for the careful reading of our manuscript and for the constructive comments. We have revised the manuscript thoroughly to improve clarity, structure, and critical depth. Our detailed responses are provided below.
Comment 1- The Web of Science search strategy, exclusion criteria, and handling of duplicates are not clearly explained. The decline in 2025 is not methodologically supported.
Response: We have revised the Bibliometric Analysis section to clearly describe the Web of Science search strategy, including the full search string, search fields (title, abstract, and keywords), language and document-type filters, and the time span considered. We have also clarified the screening process applied to titles and abstracts. The lower publication count for 2025 is now explicitly explained as a result of incomplete indexing at the time of data retrieval, rather than a confirmed decline in research activity.
Comment 2: The bibliometric analysis remains descriptive and does not clearly justify the selection of molecular approaches.
Response: We have strengthened the interpretation of the bibliometric results by explicitly linking keyword co-occurrence and MCA findings to the thematic gaps identified in the literature. A new concluding paragraph has been added to the bibliometric section explaining how the weak representation of molecular, omics, and precision tools directly informed the structure and focus of the subsequent sections of the review.
Comment 3: Omics studies are listed, but their mechanistic contributions are not discussed in depth.
Response: We have revised Section 5 to strengthen mechanistic interpretation across transcriptomic, proteomic, genomic, metabolomic, and metagenomic studies. The revised text now explains how these approaches reveal molecular pathways involved in stress tolerance, lignocellulose degradation, nutrient transport, and disease resistance, with examples linking gene expression, enzyme activity, and metabolic outcomes to cultivation performance. We also clarify why integrated multi-omics approaches are more informative than isolated analyses for improving sustainable mushroom production.
Comment 4: Adaptations in arid regions and the Middle East are not sufficiently detailed.
Response: We have expanded the sections on arid and semi-arid mushrooms to include clearer discussion of environmental stressors such as water scarcity, high temperature, and nutrient-poor soils. Species-specific examples and plant–fungal symbioses relevant to desert ecosystems have been strengthened, with clearer links to sustainable cultivation potential in arid regions, including the Middle East.
Comment 5: Mycorrhizal relationships, microbiomes, and molecular regulation are presented separately without an integrated framework.
Response: We have revised Section 5 to explicitly describe how molecular regulation, microbial communities, and mycorrhizal interactions function as interconnected components of mushroom production systems. An integrative paragraph has been added to present these processes within a unified conceptual framework rather than as isolated mechanisms.
Comment 6: The review lacks critical discussion of limitations and contradictory findings.
Response: A dedicated limitations paragraph has been added to Section 5 and further expanded in Section 7. These revisions discuss strain-specific responses, challenges in scaling laboratory findings to commercial systems, variability in experimental design, and regulatory and economic constraints that limit practical adoption of advanced molecular tools.
Comment 7: The conclusion is repetitive and does not clearly outline future priorities.
Response: The conclusion has been revised to avoid repetition and to focus on forward-looking research priorities. It now highlights specific methodological needs, including multi-omics integration, validation under arid and resource-limited conditions, and stronger links between molecular insights and applied cultivation practices, as well as implications for sustainable food production.
Author Response File: 
Author Response.docx
Reviewer 2 Report
The bibliometric analysis (n=776 articles, 2021-2025) provides a quantitative foundation for identifying thematic trends and geographical biases. Coverage spans environmental sciences, biotechnology, and food technology, reflecting the field's multidisciplinary nature. However, the reliance on Web of Science alone risks overlooking relevant studies in agricultural engineering or socio-economic literature. The explicit recognition of under-represented research from arid regions (e.g., Middle East) and limited molecular approaches demonstrates critical awareness of knowledge gaps. Whilst authoritative sources like Girotto et al. (2022) on circular economy are included, the omission of recent CRISPR application studies in Pleurotus spp. (post-2023) slightly undermines molecular coverage.
The manuscript adheres to a conventional review framework: introduction → bibliometric analysis → thematic sections (adaptations, symbiosis, omics, sustainability) → challenges → conclusion. Transitions between sections are generally smooth, particularly the progression from bibliometric gaps to molecular explorations. However, the "Sustainable Production" section (Section 6) somewhat overlaps with circular economy concepts in the introduction, creating minor redundancy.
The integration of ecological insights (e.g., Terfezia–Helianthemum symbiosis) with molecular mechanisms (e.g., HSP upregulation in heat stress) exemplifies strong interdisciplinary synthesis. However, the omission of quantitative meta-analysis to compare lignin degradation rates across species represents a missed opportunity for deeper insight.
References are generally well-formatted, with 112 citations including seminal works (e.g., Boddy, 2016) and recent studies (e.g., Maini Rekdal et al., 2024). Whilst 62% of references post-date 2020, the 50% threshold for 2019–2024 publications is narrowly unmet (48% within 5 years). The explicit documentation of bibliometric methodology (databases, keywords, inclusion criteria) enhances reproducibility.
Terminology is consistently technical yet accessible (e.g., "secotioid development," "osmo-protectants"). Some phrasing leans towards redundancy (e.g., "plays a crucial role" appears 4×). Adheres to formal academic conventions overall.
The bibliometric methodology (VOSviewer, RStudio) provides transparent, replicable literature mapping. Inclusion of search strings and temporal filters enhances rigour.
The review is transparent about its methodology for the bibliometric section, making the process reproducible. The selection of case studies (like desert truffles) is justified by the data analysis. The review is highly prospective. It doesn't just summarise the past; it predicts the integration of AI, nanotechnology, and synthetic biology into mushroom farming as the next frontier for sustainability. The authors critically assess the current state of research, pointing out that while substrate optimization is well-studied, the molecular mechanisms behind stress resilience are still emerging fields. The review provides tangible value for researchers and policymakers by outlining circular economy models and specific genetic targets for breeding climate-resilient strains.
This is a high-quality review manuscript. It is timely, well-structured, and methodologically sound. It successfully integrates bibliometric data with in-depth molecular and ecological analysis to argue for the role of mushrooms in sustainable food production, particularly under climate stress.
- The quality of the illustrations in the manuscript is severely inconsistent with the quality of the submitted content; almost all of the figures are far from aesthetically pleasing, and could even be described as ugly.
- What is the logo in the bottom right corner of Figures 2 and 6? Is it related to the image content?
- How were Figures 3-6 generated? What software and parameters were used?
- After Figure 6, there are Figures 1-3 again? What's going on?
- The references contain too many deficiencies, including incomplete page numbers, species names not being italicized, and incomplete DOIs.
- Sarcodon fungi are an important group of ectomycorrhizal fungi. Please read and add the following important references that are currently missing. Exploring the molecular tapestry of Sarcodon secondary metabolites: chemical structures, activities, and biosynthesis. -Y. Liu, M. Zhang, F. Tang, H.-Q. Wang, J.-M. Gao, M. Li, et al. Mycology 2024 Pages 1-22. DOI: 10.1080/21501203.2024.2380381
Author Response
Response to Reviewer 2
We thank the reviewer for the constructive comments, which helped improve the clarity, presentation, and completeness of the manuscript. The concerns raised have been addressed as follows:
- Figure quality and aesthetics
All figures have been reviewed and updated to improve visual clarity and consistency. Figures 1–6 are provided as high-resolution images (600 dpi), and formatting has been standardized across all figures. - Logo in Figures 2 and 6
The logo visible in Figures 2 and 6 corresponds to the software used for figure generation and is included solely as a software attribution. It is not related to the scientific content of the figures. This has now been clearly clarified in the corresponding figure captions. - Figure generation (Figures 3–6)
Clarification has been added to the figure captions specifying that Figures 3–6 were generated using RStudio-based bibliometric tools and VOSviewer. - Figure numbering
Figure numbering has been carefully checked and corrected throughout the manuscript. All figures now appear in the correct sequential order and are consistently cited in the text. - Reference deficiencies
The reference list has been thoroughly revised. Missing page numbers and DOIs have been completed where available, species names have been italicized, and overall formatting has been corrected in accordance with journal guidelines. - Addition of Sarcodon reference
The reviewer-suggested reference on Sarcodon secondary metabolites as reference no 89 (Liu et al., 2024) has been added to the reference list and integrated into Section 7: Challenges and Future Directions, where it supports discussion on molecular diversity and future research needs in ectomycorrhizal fungi.
Reviewer 3 Report
The topic of this review is interesting and relevant, and the overall idea of integrating omics approaches in mushroom cultivation is appropriate. However, the manuscript requires substantial revision in terms of structure, scientific depth, and writing quality. References are inconsistently and sometimes incorrectly linked to the text, with mismatches between in-text citations and the reference list, which undermines the credibility of the review. The manuscript lacks critical thinking and synthesis: studies are reported individually, with minimal discussion of how results compare, complement, or contradict one another, and without clear conceptual links between sections. In addition, the keyword strategy appears insufficient; the absence of the term fungi likely resulted in an incomplete literature survey, making it difficult to justify the claim of a comprehensive review, especially given the low number of retrieved publications. Until these issues are resolved, the work is not ready for publication.
I suggest to delete „comprehensive“ from the title, since this is not comprehensive review, you did not addressed all studies regarding mushrooms and fungi in the last 5 years…
Introduction
Line 32: Add reference
Line 34: This is too general mentioned… What are the mechanisms of waste utilization by mushrooms? What species are the most common?
Line 39: Give detail nutritional profile… the percentage rates and ranges for example
Line 45: What are the mechanisms for breaking down complex organic polymers such as lignin and cellulose?What type of mushrooms are dominant, white rot fungi, brown rot…?
Bibliometric analysis
Line 64: Mushroom is not enough string.. You must use fungi, Basidiomycota, Ascomycota etc. as well, since this does not reflect the realistic and thorough bibliometric analysis
Line 66: Why did you selected 5 year period? For comprehensive review at least 10 years period is suggested.
Adaptations of Mushrooms to Diverse Climates and Ecosystems
Line 146: How and why did you selected the mushrooms for Table 1? What were the reasons and selection criteria?
Table 1 – I strongly suggest adding one more column, where adaptation characteristics of every species should be mentioned
Line 171: Add reference
Line 178: Reference numbered 36 is
Turgeman, T., Ben Asher, J., Roth-Bejerano, N., Kagan-Zur, V., Kapulnik, Y. & Sitrit, Y., 2011. Mycorrhizal association between 649 the desert truffle Terfezia boudieri and Helianthemum sessiliflorum alters plant physiology and fitness to arid conditions. My-650 corrhiza, 21, pp.623-630. h ps://doi.org/10.1007/s00572-011-0369-z .
It does not match to what is mentioned in the text: „Similarly Schizophyllum commune, exhibits remarkable resilience and moisture retention, adapting to both decaying wood and arid environments.36“ since there is no mention of S. commune in the reference cited. Please check all references in reference list and the connection of references to the text written.
Symbiotic and Ecological Interactions in Mushrooms
Line 205: Add reference
Lines 209 – 217: The same point as above, the reference given is not appropriate, please add the adequate reference where ectomycorrhizal relationship between desert truffles (Terfezia spp.) and Helianthemum species is mentioned and explained.
There is no critical evaluation.. no comparisons, no synthesis..
GC regulation of enzymes, nutrient exchange in symbiosis, importance of microbiomes, roles of thymol-like metabolites are reiterated multiple times across subsections with only minor variation.
Integrative Omics Approaches in Mushroom Cultivation
Lines 352 – 358: What specific gaps omics approaches address in mushroom cultivation?
Section 5.1. Synthesize common patterns accross species
Section 5.2. What are regulatory constraints, biosafety concerns, public acceptance, or technical challenges in industrial-scale mushroom cultivation?
Line 478: Add references
Comments for author File: 
Comments.pdf
Author Response
Response to Reviewer 3
We thank the reviewer for the detailed and helpful comments. The suggestions greatly assisted us in improving the structure, clarity, and scientific quality of the manuscript. All comments have been carefully addressed, as explained below.
General comment:
The manuscript has been revised to improve overall organization, clarity, and scientific depth. Links between sections have been strengthened, repetitive content has been reduced, and comparative and integrative discussion has been added where needed. All references were checked and corrected to ensure consistency between in-text citations and the reference list. In response to the reviewer’s concern about scope, the word “comprehensive” has been removed from the title, and the limitations of the literature coverage are now clearly stated and justified.
Introduction:
Missing references have been added where requested. The introduction was revised to better explain how mushrooms utilize agricultural waste, including the mechanisms involved in lignocellulose degradation and the major fungal groups responsible. Commonly cultivated and ecologically important mushroom species are now clearly mentioned. The nutritional profile of mushrooms has been expanded to include representative compositional ranges. The roles of lignin- and cellulose-degrading fungi, particularly white-rot fungi, have also been clarified.
Bibliometric analysis:
We acknowledge the reviewer’s concern regarding the keyword strategy. Although broader taxonomic terms such as “fungi,” “Basidiomycota,” and “Ascomycota” were not explicitly included, the search was intentionally designed to focus on studies related to mushroom cultivation and production, where mushrooms represent the main applied system. This approach matches the applied focus of the review. The five-year time window was chosen to highlight recent research trends rather than to provide a fully comprehensive historical overview, and this has now been clearly explained in the revised manuscript.
Adaptations of mushrooms to diverse climates and ecosystems:
The criteria used to select species for Table 1 are now clearly stated, based on climatic relevance, availability of ecological or physiological information, and importance for food, medicinal, or ecosystem functions. A new column describing adaptation characteristics has been added to the table. Missing references were included, and all citations were carefully checked for accuracy.
Symbiotic and ecological interactions in mushrooms:
Incorrect or mismatched references were corrected, including those related to Schizophyllum commune and desert truffle symbioses. Repetitive descriptions were reduced, and comparative and integrative statements were added. A synthesis paragraph has been included to explain how symbiosis, enzymatic activity, and microbiome interactions together influence mushroom ecology across arid, temperate, and boreal environments.
Integrative omics approaches in mushroom cultivation:
This section was revised to clearly explain the specific gaps addressed by omics approaches in mushroom cultivation, such as stress tolerance, substrate utilization efficiency, strain-specific performance, and disease resistance. Cross-species synthesis has been added to highlight common molecular patterns revealed by transcriptomic and proteomic studies. Regulatory, biosafety, scalability, and public acceptance challenges related to industrial use and genetically modified strains are now explicitly discussed, along with limitations linked to strain specificity and experimental variability.
In summary, the manuscript has been thoroughly revised to improve clarity, critical discussion, and scientific rigor. We believe that all concerns raised by Reviewer 3 have been fully addressed, and we are grateful for the reviewer’s constructive feedback, which significantly improved the quality of the manuscript.
Round 2
Reviewer 2 Report
The current revised manuscript is cause for concern. There are a large number of formatting errors in the species names in the references, and the DOI formats are not consistent. Additionally, what is the table identifier in the lower right corner of Figure 2 (this identifier is not mandatory, please remove it). Issues such as this were already pointed out in the previous review comments, and the author seems to have made little effort to address them.
The current revised manuscript is cause for concern. There are a large number of formatting errors in the species names in the references, and the DOI formats are not consistent. Additionally, what is the table identifier in the lower right corner of Figure 2 (this identifier is not mandatory, please remove it). Issues such as this were already pointed out in the previous review comments, and the author seems to have made little effort to address them.
Author Response
Response to Reviewer-2 Comment
Comment:
The current revised manuscript is cause for concern. There are a large number of formatting errors in the species names in the references, and the DOI formats are not consistent. Additionally, what is the table identifier in the lower right corner of Figure 2 (this identifier is not mandatory, please remove it). Issues such as this were already pointed out in the previous review comments, and the author seems to have made little effort to address them.
Response:
We sincerely thank the reviewer for carefully re-examining the manuscript and for highlighting these important formatting issues. We apologize for the inconsistencies that remained in the previous revision.
In this revised version, we have thoroughly rechecked the entire reference list and corrected all formatting issues. Specifically:
- All species names in the reference list have been carefully reviewed and are now consistently italicized where required.
- DOI formats have been standardized throughout the manuscript according to the journal guidelines.
- The table identifier previously visible in the lower right corner of Figure 2 has been removed as suggested.
We regret that these technical issues were not fully resolved in the earlier revision and appreciate the reviewer’s patience. All corrections have been made carefully and are visible in the tracked changes version of the manuscript.
We are grateful for the reviewer’s attention to detail, which has helped improve the overall presentation and consistency of the manuscript.
Author Response File: Author Response.docx
Reviewer 3 Report
Thank You for Your explanations.
In pdf file of manuscript I do not see that reference 36 is corrected. You use it for S. commune at the line number 321-323, and for Pleurotus citrino pileatus description in Table 1. It is not correct. You must check references again and make sure that everything matches.
Author Response
Response to Reviewer-3 Comment
Comment:
In pdf file of manuscript I do not see that reference 36 is corrected. You use it for S. commune at the line number 321-323, and for Pleurotus citrino pileatus description in Table 1. It is not correct. You must check references again and make sure that everything matches.
Response:
We sincerely thank the reviewer for carefully checking the reference consistency and for pointing out the incorrect use of Reference 36.
In the revised manuscript, this issue has now been corrected. The description of Schizophyllum commune (lines 203–205 in the revised version) is now supported by Reference 44. The entry for Pleurotus citrinopileatus in Table 1 is correctly supported by Reference 36.
In addition, we have conducted a comprehensive cross-check of all in-text citations against the reference list to ensure that each citation accurately corresponds to the correct source.
All corrections are visible in the tracked changes version of the manuscript.
We appreciate the reviewer’s attention to detail, which has helped improve the accuracy and consistency of the manuscript.
Author Response File: Author Response.docx
