Deterministic Processes Dominantly Shape Ectomycorrhizal Fungi Community Associated with Pinus tabuliformis, an Endemic Tree Species in China
, Jianjun Ma 4,* and Yonglong Wang 5,*
Round 1
Reviewer 1 Report
Comments and Suggestions for AuthorsAbstract
line 18: Please change represents to ‘is well recognized woody mycorrhizae host’
line 19: Please change host healthy to host health
line 20: Please change tree to species
line 20: Please start the sentence with In this study, we examined
line 25 what do you mean by high proportion? please add the relative abundance percentage here
line 29 please change governed by driven
line 29 which deterministic process? please specify
Introduction
line 38 please change symbiont with symbiosis
What do you mean by promoting nutrients? Do you mean nutrient allocation to the host?
line 40 please remove the statement about water mobilization, this is not one of the fundamental roles ectomycorrhizal plays. They provide nutrient in exchange of carbon, they contribute to Carbon sequestration in soil
Materials and Methods
line 117 why didn't you measure any sand or clay content? you could have calculated OM as well since you have total carbon and N
line 154 did you use protax to help you with automozing the taxonomic identification and funguild for the functional guild identification? Please specify a part from citing the Tedersoo paper.
line 165 specaccum is defined as a function not command, please revise.
line 169 did you run the random forest with only 15 samples? you could consider using the NMDS axis1 and correlate it to the abiotic factors.
line 203 please change preferences to respond to specific environmental conditions.
line 210 please revise the term preference, it seems to me non-technical at all.
line 230 did you rarefy to calculate diversity or also for composition? please specify, however for composition you don't need to rarefy if you transformed the data to hellinger.
line 232 did you try to identify other guilds like saprotrophs, plant pathogens, yeasts and molds?
figure 2 please improve figure 2, the quality is quite low and try to color each set and intersection so that is more understandable.
figure 4 is others representing taxa that are not EM? If this is the case, how is it possible that the abundance is so low? Did you also include the unknown taxa? otherwise the relative abundance is quite biased.
figure 7 figure quality could be improved.
line 338-343 please rephrase these sentences because they are not clear.
please include a Conclusion paragraph highlighting the main finding and possible future research lines.
Comments for author File: 
Comments.pdf
English language could be improved by another round of revisions by the authors.
Author Response
Thank you for pointing this out. We agree with these comments. All the review comments have been addressed by making corresponding revisions in the relevant sections of the manuscript. The quality of the figures and tables has been enhanced. Meanwhile, appropriate responses and explanations have been provided for the questions raised by the reviewers.
Author Response File: Author Response.pdf
Reviewer 2 Report
Comments and Suggestions for AuthorsThe manuscript represents a significant and interesting study on the ECM fungi associated with Pinus tabuliformis. Overall, it is well-written, logically structured, and the methods applied are appropriate for addressing the research question. My main comments mostly concern the description of the bioinformatic methods and the presentation of the results. Please, see my detailed suggestions below.
- The title is very long. I would recommend shortening it without losing too much information. For example: “Deterministic processes shape ectomycorrhizal fungi community associated with Pinus tabuliformis, an endemic tree species in China.”
- Avoid repeating words from the title in the keywords to improve search algorithm visibility.
- Line 106: The number of study sites is not specified. Please, include the exact number and name each site within this paragraph. Additionally, more details on the sampling range are needed, such as coordinates for each sampled tree. Further information about the sampling locations should also be provided. Notably, there is a significant difference in the number of detected OTUs between sites, particularly between CF and WLS. This variation may stem from differences in sampling strategy. Unfortunately, soil characteristics were not measured at all 15 locations, limiting the ability to assess within-site variation. As a supplement, consider including a barplot for each individual sample (similar to Figure 4). With only 15 samples, such a figure would remain clear and informative.
- Line 128: Typo in “hphae”.
- Line 145: Were the reads indeed 250 and not 300 bp long (you used PE300)?
- Report the used versions for all used programs and packages.
- Additional information on library quality is needed. Please include a MultiQC report for filtered reads as supplementary material. This can be easily generated using the free tools “FastQC” followed by “MultiQC.” I would have run it myself using your data, but the samples on NCBI are not properly labelled, making it impossible to assign them to specific sites. To resolve this, please update Table S1 to include sample identifiers along with their corresponding site information and geographic coordinates.
- Critical information about each analyzed sample—such as geographic coordinates, soil parameters, and NCBI accession numbers—is missing, making it difficult to assess the robustness of the sampling strategy. The accumulation curve (Figure 1A) raises concerns, particularly for the CF site, highlighting the need for stronger justification that sampling was sufficient to support the study's conclusions. Additionally, Figure 8 indicates that for the CF site, stochastic and deterministic processes contribute nearly equally to fungal community assembly, with MST values close to 50%. As such, the conclusion regarding the dominance of deterministic processes currently appears somewhat overstated.
- In general, paragraph 2.4 is not detailed enough. Please, provide parameters for the read filtering, identity threshold against UNITE db, the version of the db used and so on.
- Line 196: Did you use rarefied reads?
- Figure S2: Please, add the label for the x-axis.
- Line 258: Genus names are not italicized as required.
- 6: The x-axis label doesn’t have to be abbreviated. “Significant factors shown in red” is a bit confusing since they all are red. You can simply write that they all are significant. Units for most of the variables are missing.
- Figs 2 and 7 look stretched for some reason.
- Fig.8: What are the PF and PP abbreviate?
Author Response
Thank you for pointing this out. We agree with these comments. All the review comments have been addressed by making corresponding revisions in the relevant sections of the manuscript. The quality of the figures and tables has been enhanced. Meanwhile, appropriate responses and explanations have been provided for the questions raised by the reviewers.
Author Response File: Author Response.pdf
Round 2
Reviewer 2 Report
Comments and Suggestions for AuthorsThe authors have addressed most of the comments; however, the most critical issue, Comment 7 from the previous review, remains unresolved. The sequences deposited in GenBank still cannot be matched to their corresponding samples and locations. GenBank lists only two locations (China: Chifeng and China: Bayannaoer), while the manuscript refers to three sites (CF, Chifeng; HLK, Heilihe; WLS, Wulashan). To ensure reproducibility of this study, please provide in the S1 table the GenBank sample/library name alongside the corresponding sample origin for each of the 15 samples.
Additionally, no information on the final read quality and quantity per library/sample has been provided as supplemental material (e.g., a MultiQC report), as was previously requested.
Author Response
Comments 1: [The authors have addressed most of the comments; however, the most critical issue, Comment 7 from the previous review, remains unresolved. The sequences deposited in GenBank still cannot be matched to their corresponding samples and locations. GenBank lists only two locations (China: Chifeng and China: Bayannaoer), while the manuscript refers to three sites (CF, Chifeng; HLK, Heilihe; WLS, Wulashan). To ensure reproducibility of this study, please provide in the S1 table the GenBank sample/library name alongside the corresponding sample origin for each of the 15 samples.]
Response 1: We have added related information of NCBI in Table S1.
Comments 2: [Additionally, no information on the final read quality and quantity per library/sample has been provided as supplemental material (e.g., a MultiQC report), as was previously requested.]
Response 2: Thanks for your suggestion here. As the sequencing work was conducted about five years ago by the Chengdu Institute of Biology, Chinese Academy of Sciences, which only provided us the raw data and clean data files. We have checked and added the information on number of sequences in raw data and clean data. Please see Table S2.
Author Response File: Author Response.pdf
