Impact of Stump Removal on Communities of Ectomycorrhizal and Other Soil Fungi in Norway Spruce Stands of Latvia
Round 1
Reviewer 1 Report
Long-term studies add to existing knowledge, especially due to the use of new research methods, but the article also has some inaccuracies:
Some words are used, the meaning of which is not entirely precise or clear (such as in lines 24-26: „Fungi from Heterobasidion annosum species complex cause root rot and stem decay of many coniferous and some deciduous trees in Northern Hemisphere, solemnly in Europe causing economic losses more than 500 million Euro””; lines 40, 46: “stump extraction”).
There are many mistakes in the text - the writing of dashes is different - it is not clear when there should be a long dash between the numbers and when a short one (like for example lines 12, 36 and 39) or spaces between numbers are needed to indicate a citation (like for example lines 12, 26, 34 and 43), whether lines should be separated by spaces (such as lines 36, 39, 59, 63), etc.
Errors in formulas or symbols should be corrected (like line 95: „18 µl of ddH2O per sample were used”; line 99: “DNA synthesis - 72oC for 1 min; final synthesis - 72oC 10 min., etc.).
Latin names must be written in italics (lines 161-165: Thelephora terrestris, Inocybe lacera, etc.).
Author Response
Response to reviewer 1 comments
English language and style were edited by native English speaker Dr. Dainis Rungis.
- question: Some words are used, the meaning of which is not entirely precise or clear (such as in lines 24-26: „Fungi from Heterobasidion annosum species complex cause root rot and stem decay of many coniferous and some deciduous trees in Northern Hemisphere, solemnly in Europe causing economic losses more than 500 million Euro””; lines 40, 46: “stump extraction”).
Response: corrected.
2. Question. There are many mistakes in the text - the writing of dashes is different - it is not clear when there should be a long dash between the numbers and when a short one (like for example lines 12, 36 and 39) or spaces between numbers are needed to indicate a citation (like for example lines 12, 26, 34 and 43), whether lines should be separated by spaces (such as lines 36, 39, 59, 63), etc.
Response: corrected
Question 3. Errors in formulas or symbols should be corrected (like line 95: „18 µl of ddH2O per sample were used”; line 99: “DNA synthesis - 72oC for 1 min; final synthesis - 72oC 10 min., etc.).
Response: corrected
Question 4. Latin names must be written in italics (lines 161-165: Thelephora terrestris, Inocybe lacera, etc.).
Response: corrected.
Reviewer 2 Report
The authors studied the impact of stump removal on community of ectomycorrhizal and other soil fungi in Norway spruce stands of Latvia. This is a good topic deserving investigation. However, there are some drawbacks that should be addressed. I’m sorry I can’t recommend its acceptance.
The first problem is that soil fungal communities were studied, but the results in Section 3 did not provide the community structure (abundance, richness, diversity) of the fungi. The current data of results were too simple.
Second, the structure of the manuscript was unclear. In my opinion, Introduction section can be divided into some paragraphs. Sub-titles should be added in Sections 2 and 3, which will make the structure more clear.
Third, the language should be improved.
Other minor suggestions:
Introduction: This is a long paragraph, which can be divided into two or three.
L12: correct “were” as “was”
L18: correct “was” as “were”. Please check the language.
L49: wrong grammar; “was made”?
L58: Divide Section 2 Materials and methods into some sub-sections, which will make the structure more clear.
L63-69: describe the climate conditions;
L70: A new paragraph here.
L82: What are “roots and tree roots”? How to confirm the roots are you want to sample? Not the roots of other plants?
L144: Results can be divided into several sub-sections (3.1., 3.2…).
L169: Please provide statistical results (mean ±SD) of Shannon index using a table or figure.
L184-185: Please provide Shannon index
Results: Why not provide the relative abundance of these determined fungi at genus level?
Author Response
English language and style were edited by native English speaker Dr. Dainis Rungis.
Question 1. The first problem is that soil fungal communities were studied, but the results in Section 3 did not provide the community structure (abundance, richness, diversity) of the fungi. The current data of results were too simple.
Response: Added: The data from our study show that the total number of fungal taxonomic units and the Shannon diversity indices did not differ between stump removal and control samples (Figure 2 and 3, respectively). , also figure 5 added.
Question 2: Second, the structure of the manuscript was unclear. In my opinion, Introduction section can be divided into some paragraphs. Sub-titles should be added in Sections 2 and 3, which will make the structure more clear.
Response: Done as suggested.
3. question: Third, the language should be improved.
Response: English language and style were edited by native English speaker Dr. Dainis Rungis.
Other minor suggestions:
4. Question: Introduction: This is a long paragraph, which can be divided into two or three.
Response: Done
L12: correct “were” as “was”
Response: Corrected
L18: correct “was” as “were”. Please check the language.
Response: cerrected
L49: wrong grammar; “was made”?
Response: Corrected
L58: Divide Section 2 Materials and methods into some sub-sections, which will make the structure more clear.
Response: Done as suggested
L63-69: describe the climate conditions;
Response: added 'The territory of Latvia is characterized by a temperate climate. Sampling areas were located in Central Latvia, where the average annual temperature ranges from 6.8 to 7.9ËšC and annual precipitation rate is 574 to 636 mm.'
L70: A new paragraph here.
Response: Done as suggested
L82: What are “roots and tree roots”? How to confirm the roots are you want to sample? Not the roots of other plants?
Response: Corrected 'In each sample plot, the average growth rates of saplings (height and diameter), as well as tree species composition were assessed, and soil samples collected from five spruce saplings growing in each sub - sample plot. Soil samples were collected at a depth of 20 cm using a soil probe (30). A total of 60 soil samples were collected: 30 samples from the stump removal plots and 30 samples from the control plots.'
L144: Results can be divided into several sub-sections (3.1., 3.2…).
Response: Done as suggested
L169: Please provide statistical results (mean ±SD) of Shannon index using a table or figure.
Response: Figures 2,3 and 4 were added
L184-185: Please provide Shannon index
Response: Figures 2,3 and 4 added
Results: Why not provide the relative abundance of these determined fungi at genus level?
Response: Fungal abundance provided in Table 1.
Reviewer 3 Report
This manuscript "Impact of stump removal on the community of ectomycorrhizal and other soil fungi in Norway spruce stands of Latvia" is an interesting piece of work worth to be considered in Diversity but it needs some revisions before it is accepted. The comments and suggestions are annotated in the PDF. The authors are encouraged to get a native English speaker to read the manuscript before resubmitting it.
Comments for author File: 
Comments.pdf
Author Response
Question 1: Language revision
Response 1: English language and style were edited by native English speaker Dr. Dainis Rungis.
Question 2. Please provide location names.
Response: Location names added.
Round 2
Reviewer 2 Report
The authors have made some revisions. However, I can't understand richness residuals (Fig. 2 and Fig. 5) and Shannon residuals (Fig. 3). Please provide equations that used to calculate them in materials and methods. As far as I know, the common richness index is ACE index and Chao1 index. Use Shannon index to replace Shannon residuals.
Author Response
Reviewers comment: However, I can't understand richness residuals (Fig. 2 and Fig. 5) and Shannon residuals (Fig. 3). Please provide equations that used to calculate them in materials and methods. As far as I know, the common richness index is ACE index and Chao1 index. Use Shannon index to replace Shannon residuals.
Response: To facilitate reader, we have substituted residuals to original input values. We still find residuals as a good way to present sequencing data because it normalizes data set and integrates sequencing depth which can strongly vary among samples and sequencing runs. Sentence we have added (and now removed) from M&M explained calculation and use of this approach by other authors (“For statistical analysis, measures of OTU (Operational taxonomic unit) richness and Shannon diversity indices were converted to residuals based on the average values of raw residuals taken from regression analyses of OTU richness or Shannon diversity index vs. square-root-transformed sequencing depth and log-transformed sequencing depth [26]”). However, we agree that our data set is provided by the same run and therefore, probably, such transformation can be excluded.
We have changed indicated figures to input data without transformations.
