Analysis of Basidiomycete Fungal Communities in Soil and Wood from Contrasting Zones of the AWPA Biodeterioration Hazard Map across the United States
, Amy B. Bishell 1, Jed Cappellazzi 2, Samuel V. Glass 1, Jonathan A. Palmer 3, Nathan J. Bechle 1 and William J. Hickey 4,†
Round 1
Reviewer 1 Report
Comments and Suggestions for AuthorsI have had the opportunity to review the manuscript titled "Analysis of Basidiomycete Fungal Communities in Soil and Wood Across Contrasting Zones of the AWPA Biodeterioration Hazard Map in the United States." Overall, the manuscript provides valuable insights into the diversity and composition of basidiomycete fungi, particularly in relation to wood decay across different zones outlined by the AWPA hazard map.
The study addresses an important research gap regarding the lack of comprehensive information on fungal communities in soil and wood, particularly concerning their diversity and abundance across different hazard zones.
However, while the study's contribution is significant, there are a few aspects that I believe could be further improved:
Stress Test: Although the low variance percentages in the axes diminish the clarity of the NMDS plots, it is expected in this kind of data with so many dimensions. However, the absence of stress values in the NMDS ordinations is a notable gap. This metric is vital in assessing the goodness of fit in ordination analyses. Correct if I’m wrong, but I don’t think the authors mentions this test anywhere in the manuscript.
OTUs vs. ASVs: Given the increased accuracy and resolution of ASVs, especially in distinguishing closely related taxa, I would like a comment from the authors justifying the preference for OTUs.
Figure Improvements: Figures in the manuscript, especially the NMDS ordination plots, require substantial enhancement. The legends and labels on the axes are unclear.
Method Simplification: The methods section appears overly detailed. Simplification without compromising essential information is advisable. For example, in lines 145-149: “AmpTk is a series of scripts… Ion Torrent, MiSeq, and 454 data [27].”, I don’t think this information is essential, as well as explaining all the diversity indexes, among other things.
Overall, the manuscript presents valuable insights into fungal communities across hazard zones. Addressing the identified concerns, particularly stress test inclusion and clearer figure legends, will significantly strengthen the manuscript.
Author Response
Reviewer 1:
I have had the opportunity to review the manuscript titled "Analysis of Basidiomycete Fungal Communities in Soil and Wood Across Contrasting Zones of the AWPA Biodeterioration Hazard Map in the United States." Overall, the manuscript provides valuable insights into the diversity and composition of basidiomycete fungi, particularly in relation to wood decay across different zones outlined by the AWPA hazard map.
The study addresses an important research gap regarding the lack of comprehensive information on fungal communities in soil and wood, particularly concerning their diversity and abundance across different hazard zones.
However, while the study's contribution is significant, there are a few aspects that I believe could be further improved:
Stress Test: Although the low variance percentages in the axes diminish the clarity of the NMDS plots, it is expected in this kind of data with so many dimensions. However, the absence of stress values in the NMDS ordinations is a notable gap. This metric is vital in assessing the goodness of fit in ordination analyses. Correct if I’m wrong, but I don’t think the authors mentions this test anywhere in the manuscript.
Thank you for the comment and you are absolutely correct. Stress values have been added to the ordinations and discussed within the text (see lines 275-277)
OTUs vs. ASVs: Given the increased accuracy and resolution of ASVs, especially in distinguishing closely related taxa, I would like a comment from the authors justifying the preference for OTUs.
Very valid comment, a new section discussing our rationale for using OTUs as opposed to ASVs throughout the manuscript.
Figure Improvements: Figures in the manuscript, especially the NMDS ordination plots, require substantial enhancement. The legends and labels on the axes are unclear.
New figures were included with higher resolution to address the reviewer comments, this was also brought up by reviewer 3.
Method Simplification: The methods section appears overly detailed. Simplification without compromising essential information is advisable. For example, in lines 145-149: “AmpTk is a series of scripts… Ion Torrent, MiSeq, and 454 data [27].”, I don’t think this information is essential, as well as explaining all the diversity indexes, among other things.
The sentence in lines 145-149, the authors agree and have removed the sentence. .
Overall, the manuscript presents valuable insights into fungal communities across hazard zones. Addressing the identified concerns, particularly stress test inclusion and clearer figure legends, will significantly strengthen the manuscript.
Thank you for the suggested improvements, I have addressed each of these comments and feel that the manuscript is much improved.
Reviewer 2 Report
Comments and Suggestions for AuthorsThe manuscript is well written and documented. Manuscript publication is recommended. The only suggestion is to improve the references by adding a few more references from the last 5 years of citations.
Author Response
The manuscript is well written and documented. Manuscript publication is recommended. The only suggestion is to improve the references by adding a few more references from the last 5 years of citations.
Thank you for the recommendation, we have added several new citations to bring the manuscript more up to date.
Reviewer 3 Report
Comments and Suggestions for AuthorsI have reviewed the manuscript titled "Analysis of basidiomycete fungal communities in soil and wood from contrasting zones of the AWPA biodeterioration hazard map across the United States" by Kirker et al., submitted for publication in Forests. The manuscript addresses an important issue regarding wood deterioration by basidiomycetous decay fungi and the effectiveness of preservative treatments. It provides valuable insights into the diversity and abundance of these fungi in different zones of the AWPA hazard map. Overall, I find the manuscript to be well-written and scientifically sound, but I have a few comments and suggestions that need to be addressed before it can be considered for publication.
The abstract could be improved by providing a brief overview of the methodology and key results.
The introduction should clearly articulate the broader relevance of the study to the field of wood preservation and biodeterioration, emphasizing why this research is important.
Results could benefit from clearer graphical representations (e.g., figures or tables) to enhance the understanding of the findings.
The discussion section is informative but could be strengthened by comparing the results obtained from the three-zone AWPA hazard map with those from the previous five-zone hazard map. Additionally, the ecological implications of the findings for wood decay and preservation should be discussed in more detail.
There is no conclusion section
Comments on the Quality of English LanguageMinor editing of English language required
Author Response
Reviewer 3:
I have reviewed the manuscript titled "Analysis of basidiomycete fungal communities in soil and wood from contrasting zones of the AWPA biodeterioration hazard map across the United States" by Kirker et al., submitted for publication in Forests. The manuscript addresses an important issue regarding wood deterioration by basidiomycetous decay fungi and the effectiveness of preservative treatments. It provides valuable insights into the diversity and abundance of these fungi in different zones of the AWPA hazard map. Overall, I find the manuscript to be well-written and scientifically sound, but I have a few comments and suggestions that need to be addressed before it can be considered for publication.
The abstract could be improved by providing a brief overview of the methodology and key results.
Abstract was revised in an attempt to provide the aforementioned results.
The introduction should clearly articulate the broader relevance of the study to the field of wood preservation and biodeterioration, emphasizing why this research is important.
The introduction was improved in an attempt to articulate the broader relevance of the study to the field of wood preservation, see line 75-76.
Results could benefit from clearer graphical representations (e.g., figures or tables) to enhance the understanding of the findings.
All figures have been updated to improve their resolution.
The discussion section is informative but could be strengthened by comparing the results obtained from the three-zone AWPA hazard map with those from the previous five-zone hazard map. Additionally, the ecological implications of the findings for wood decay and preservation should be discussed in more detail.
A new paragraph was added in order to expound on this subject.
There is no conclusion section
A new conclusion section was added so summarize the results of our study. It does significantly improve readability.
Additional changes: NCBI Accession numbers were added as well as documentation on source of funding.
Round 2
Reviewer 3 Report
Comments and Suggestions for AuthorsThe manuscript has been improved and no further revisions are necessary.
