Amazonian Fungal Diversity and the Potential of Basidiomycetes as Sources of Novel Antimicrobials

Round 1

Reviewer 1 Report

Comments and Suggestions for Authors

This manuscript presents a comprehensive knowledge framework that highlights the value of Amazonian Basidiomycetes as a promising source for novel biotechnological and pharmaceutical applications. The authors examine fungal diversity and chemical potential and identify the need to increase research efforts to assess this largely untapped resource. Overall, the manuscript identifies knowledge gaps and outlines a roadmap for future taxonomic, ecological, and genomic research on Amazonian Basidiomycetes, underscoring their importance for conservation. 

The manuscript is well-written and provides a baseline reference for compiling major contributions to research on Amazonian Basidiomycetes. The literature coverage is adequate, and the topic aligns well with current interests in tropical fungal diversity. However, I would recommend mentioning major efforts in the region to create biorepositories, sampling efforts, and limitations.  

Author Response

Reviewer 1

 

Reviewer 1, Comment1- This manuscript presents a comprehensive knowledge framework that highlights the value of Amazonian Basidiomycetes as a promising source for novel biotechnological and pharmaceutical applications. The authors examine fungal diversity and chemical potential and identify the need to increase research efforts to assess this largely untapped resource. Overall, the manuscript identifies knowledge gaps and outlines a roadmap for future taxonomic, ecological, and genomic research on Amazonian Basidiomycetes, underscoring their importance for conservation. 

The manuscript is well-written and provides a baseline reference for compiling major contributions to research on Amazonian Basidiomycetes. The literature coverage is adequate, and the topic aligns well with current interests in tropical fungal diversity. However, I would recommend mentioning major efforts in the region to create biorepositories, sampling efforts, and limitations.  

 

Authors’ Response: We thank the reviewer for this valuable suggestion. In the revised manuscript, we addressed this point explicitly in Section 5: “Limitations and Future Research Directions” (lines 527–544) by (i) highlighting the importance of strengthening biorepositories and curated culture collections (including long-term preservation, vouchering, and data-sharing practices), (ii) emphasizing a need for expanding systematic sampling efforts across major Amazon ecosystems and seasons, ideally through coordinated, network-based frameworks, and (iii) clearly acknowledging key limitations that currently constrain progress in the region, including access and logistics, permitting and access-and-benefit-sharing requirements, taxonomic bottlenecks, and the scarcity of reference sequences and genomes for reliable species-level assignments.

Reviewer 2 Report

Comments and Suggestions for Authors

I would like to say that this manuscript needs to address major revision before publishing in ‘Biology’. In my opinion, the work is compelling as it effectively summarizing current knowledge regarding fungal diversity across major Amazon ecosystems and their role for producing natural molecules with antimicrobial activity. However, the manuscript lacks several important aspects that must be addressed before publishing in the current journal such as;

1. Line 126. The section 2 needs to be divided into two sub-sections. One sub-section should revolve around general diversity of fungi, while the other sub-section specifically tells about the basidiomycetes diversity. However, focus should be given more to diversity of the basidiomycetes. I would suggest to discuss the diversity under genus level (major genera) headings, so far reported from the same habitats.
2. I would suggest to add an another heading after the diversity section which focuses on the general activities of basidiomycetes in Amazon ecosystems that what are they doing naturally in this habitat e.g. decomposition etc.?
3. Line 274. A new heading before section 3 needs to introduced regarding why do basidiomycetes preferred over other fungi for antimicrobial potentials in this manuscript? A proper justification is needed here.
4. Line 275. Like section 3.1, another section is required to be added about the fungal pathogenicity, resistance to drugs, dangers to health etc. as metabolites from basidiomycetes are also discussed as antifungal in the current manuscript.
5. Line 304. The classes of the antimicrobial metabolites should be divided into various sub-headings and discussed in details regarding their potential against various pathogens under the section 3 e.g. terpenes, steroids, anthraquinones, alkaloids, peptides, and phenolic metabolites etc.
6. Line 379. The section 3.3 needs re-structuring as it lacks many important aspects. First, this portion should be dedicated to basidiomycetes only as the current first paragraph is telling the story of actinomycetes. Second, the pathway should be generally discussed in details first and then, specifically discussed pathway for any of the metabolite e.g. terpenes (specific type), in details by taking example of the well-studied fungus of basidiomycetes.
7. The authors need to revised the entire manuscript for any English grammar mistakes in the manuscript.

Best wishes,

Comments on the Quality of English Language

The authors need to revised the entire manuscript for any English grammar mistakes in the manuscript.

Author Response

Reviewer 2

Reviewer 2, Comment 1- I would like to say that this manuscript needs to address major revision before publishing in ‘Biology’. In my opinion, the work is compelling as it effectively summarizing current knowledge regarding fungal diversity across major Amazon ecosystems and their role for producing natural molecules with antimicrobial activity. However, the manuscript lacks several important aspects that must be addressed before publishing in the current journal such as;

Authors’ Response: We thank the reviewer for the careful evaluation of the manuscript and for recognizing its relevance. All comments raised were carefully considered, and the manuscript was substantially revised to improve its structure, clarity, and scientific focus, as detailed in the point-by-point responses below.

 

Reviewer 2, Comment 2- Line 126. The section 2 needs to be divided into two sub-sections. One sub-section should revolve around general diversity of fungi, while the other sub-section specifically tells about the basidiomycetes diversity. However, focus should be given more to diversity of the basidiomycetes. I would suggest to discuss the diversity under genus level (major genera) headings, so far reported from the same habitats.

Authors’ response: We thank the reviewer for this constructive recommendation. We have restructured Section 2 (Fungal Biodiversity in the Amazon) into two major subsections: (i) general fungal diversity across Amazon ecosystems and (ii) “3. Basidiomycetes Diversity and Ecological roles in the Amazonian eco-system”. The Basidiomycetes-focused subsection was expanded and organized focusing on genus-level headings (major genera) and associated habitats, providing a clearer synthesis with emphasis on Basidiomycetes. Modifications have been highlighted in yellow.

 

Reviewer 2, Comment 3- I would suggest to add an another heading after the diversity section which focuses on the general activities of basidiomycetes in Amazon ecosystems that what are they doing naturally in this habitat e.g. decomposition etc.?

Authors’ response: We agree with the reviewer and added chapter “3. Basidiomycetes Diversity and Ecological roles in the Amazonian eco-system”, highlighting the main genera of fungi involved and their natural functions (lignocellulosic decomposition, nutrient cycling, and competitive interactions on wood and litter), and using this ecological context to better frame antimicrobial bioprospecting. Modifications have been highlighted in yellow.

 

Reviewer 2, Comment 4- Line 274. A new heading before section 3 needs to introduced regarding why do basidiomycetes preferred over other fungi for antimicrobial potentials in this manuscript? A proper justification is needed here. 

Authors’ response: We thank Reviewer 3 for this helpful suggestion. Instead of adding a new heading, we inserted a concise justification paragraph as the first paragraph of Section 3 to clarify our focus. The revision explains that basidiomycetes are highly diverse yet comparatively underexplored regarding their antimicrobially active chemistry, especially versus commonly studied ascomycetes. We also highlight Amazonian ecological pressures and emerging omics evidence supporting substantial cryptic biosynthetic potential in basidiomycetes. Modifications have been highlighted in yellow.

 

 

Reviewer 2, Comment 5- Line 275. Like section 3.1, another section is required to be added about the fungal pathogenicity, resistance to drugs, dangers to health etc. as metabolites from basidiomycetes are also discussed as antifungal in the current manuscript.

Authors’ response: We expanded section 3.1 (now, Section 4.1) to include a new paragraph on the global burden of fungal diseases and antifungal resistance, referencing priority fungal pathogens and emphasizing an urgent need for novel antifungal agents, thus strengthening the rationale for basidiomycete-derived antifungal metabolites. Modifications have been highlighted in yellow.

 

 

Reviewer 2, Comment 6- Line 304. The classes of the antimicrobial metabolites should be divided into various sub-headings and discussed in details regarding their potential against various pathogens under the section 3 e.g. terpenes, steroids, anthraquinones, alkaloids, peptides, and phenolic metabolites etc.

Authors’ response: We thank the reviewer for this suggestion. We reorganized the metabolite section focusing on chemical classes (e.g., terpenoids, steroids, polyketides/quinones, alkaloids, peptides, phenolics). For each class, we expanded the narrative to better relate representative molecules to reported antimicrobial spectra and target pathogens, supported by Table 4. Modifications have been highlighted in yellow.

 

 

 

Reviewer 2, Comment 7- Line 379. The section 3.3 needs re-structuring as it lacks many important aspects. First, this portion should be dedicated to basidiomycetes only as the current first paragraph is telling the story of actinomycetes. Second, the pathway should be generally discussed in details first and then, specifically discussed pathway for any of the metabolite e.g. terpenes (specific type), in details by taking example of the well-studied fungus of basidiomycetes.

Authors’ Response: We thank the reviewer for this valuable critique. We revised section 3.3 (now 4.3) to focus strictly on Basidiomycetes. The actinomycetes references were removed. Now, we first describe the major biosynthetic routes in Basidiomycetes (MVA, PKS, NRPS, shikimate/tryptophan-related pathways) and then provide a more detailed pathway example focusing on a representative Basidiomycete-derived terpenoid.

 

 

Reviewer 2, Comment 8- The authors need to revised the entire manuscript for any English grammar mistakes in the manuscript.

Authors’ Response: We thank the Editorial Office for this recommendation. The manuscript has been thoroughly revised for English language clarity and grammar. In particular, Prof. Dr. Hagen Frickmann performed a new English revision to ensure that the revised version is fully aligned with the journal’s standards.

Reviewer 3 Report

Comments and Suggestions for Authors

Introduction

Lines 92-93: which origins date back approximately 100 million years” Correction’ whose origins date back …

Section 2.1:

Section 2.3

Line 224: “Environmental DNA (eDNA) s Samples…replace please “Environmental DNA (eDNA) samples…

Figure 2

Lines 255-261: Comment: The disclosure regarding AI-assisted image generation is transparent and appropriate. However, consider shortening slightly to improve readability. Please replace all figures: 1, 2 and 3 with original images???

Section 3.1

Line 287: underscoring the need of identifying innovative. Correction suggested: underscoring the need to identify innovative”

Figure 3

Line 316: Comment: Pleurotus ostreatus is widely cultivated and may not be strictly Amazonian. Please, consider clarifying whether images represent Amazonian collections or generic representatives.

Discussion section

Conclusions

Lines 544-546: whose biosynthesis involve pathways” Correction: whose biosynthesis involve(s) pathways.

-season-depending” replace with ‘season-dependent’ (line 242)

-interfere with the progress” correct “interfere with progress (line 501)

-help identifying” change with ‘help identify’ (line 490)

Accept after minor revision

Author Response

Reviewer 3

 

Introduction

Lines 92-93: which origins date back approximately 100 million years” Correction’ whose origins date back …

Author´s answer = We thank the reviewer for pointing out this grammatical issue. The phrase has been corrected from “which origins date back approximately 100 million years” to “whose origins date back approximately 100 million years”.

 

Section 2.1:

Section 2.3

Reviewer 3, Comment 2= Line 224: “Environmental DNA (eDNA) s Samples…replace please “Environmental DNA (eDNA) samples…

 

Author´s answer: We have carefully checked the wording in line 224 and confirmed that the expression now consistently reads “Environmental DNA (eDNA) samples”, with no typographical or formatting issues.

 

Figure 2

Reviewer 3, Comment 2= Lines 255-261: Comment: The disclosure regarding AI-assisted image generation is transparent and appropriate. However, consider shortening slightly to improve readability. Please replace all figures: 1, 2 and 3 with original images???

 

Author´s answer:  We thank the reviewer for this suggestion. The disclosure regarding AI-assisted image generation was shortened while maintaining transparency and compliance. Figures 1 and 3 are original photographs from the authors’ archive, whereas Figure 2 is a schematic representation generated with AI assistance and scientifically validated by the authors, as stated in the legends.

 

 

Section 3.1

Reviewer 3, Comment 4= Line 287: underscoring the need of identifying innovative. Correction suggested: underscoring the need to identify innovative”

Author´s answer:  We thank the reviewer for this correction. The sentence has been revised accordingly.

 

 

Figure 3

Reviewer 3, Comment 5= Line 316: Comment: Pleurotus ostreatus is widely cultivated and may not be strictly Amazonian. Please, consider clarifying whether images represent Amazonian collections or generic representatives.

Author´s answer: = We thank the reviewer for this important comment. We have revised the Figure 3 legend to clarify that the photographs depict basidiomycete specimens collected by the authors in the Adolpho Ducke Forest Reserve (Manaus, Brazilian Amazon) in April 2023, and that the images are from the authors’ own archive. This clarification ensures that the figure represents Amazonian collections rather than generic cultivated material.

 

Discussion section

Conclusions

Reviewer 3, Comment 6= Lines 544-546: whose biosynthesis involve pathways” Correction: whose biosynthesis involve(s) pathways.

Author´s answer: = We thank the reviewer for this correction. The phrase has been revised to “whose biosynthesis involves pathways.

 

Reviewer 3, Comment 7= -season-depending” replace with ‘season-dependent’ (line 242)

Author´s answer: = We thank the reviewer for this correction. The phrase has been revised accordingly.

 

Reviewer 3, Comment 8= -interfere with the progress” correct “interfere with progress (line 501)

Author´s answer: = We thank the reviewer for this correction. The phrase has been revised accordingly.

 

Reviewer 3, Comment 9= -help identifying” change with ‘help identify’ (line 490)

Author´s answer: = We thank the reviewer for this correction. The phrase has been revised to “whose biosynthesis involves pathways.

 

Reviewer 3, Comment 10= Accept after minor revision

Author´s answer: We thank the reviewer for the corrections provided. All suggested changes have been implemented in line with the suggestions.

Round 2

Reviewer 2 Report

Comments and Suggestions for Authors

The comments and suggestions given previously have thoroughly been addressed by authors. Now, the manuscript seems fit to be accepted for publication in its present form.