Effects of Edaphic Factors at Different Depths on β-Diversity Patterns for Subtropical Plant Communities Based on MS-GDM in Southern China
Round 1
Reviewer 1 Report
This manuscript focused on the effects of soil the beta diversity patterns in Nanling Mountain, and found that soil chemical properties got great influence on beta diversity in this area, especially to the trees. The study is suitable for publication in Forests, however, I do not think this version is ready to be accepted. I have some comments and suggestions, listed as follows:
Introduction:
1,Accoring to the context, I think “continent and aquatic ecosystems” should be “terrestrial and aquatic ecosystems”;
1,In paragraph 2, why not refer to the literature on beta diversity of legendre, et al 2009 on Ecology;
3,Change all the “fixed plot” to “dynamic plot”;
Methods
4,In paragraph 1. “The study site was established in 2017 following CTFS standand census protocpls”. This sentence is wired to be here. Please move to the next paragraph;
5,I suggest to add a map of the plots locations so that we can just see where the sample locations are and the distance between them;
6,In “soil sampling and analysis”, the format “Lu Rukun,2000” should be modified;
7,Since there were 24 plots (including 21 forest plots and 3 mountain scrubby-meadow plots), Why the Bray-Curtis distance matrix were 18*18? And, I did not get the relationship between Bray-Curtis distance matrix and Sørensen dissimilarity index. If there was indeed no relationship between them, please move the Bray-Curtis distance matrix to the MS-GDM model paragraph;
Results
8,“By calculating the Bray-Curtis distance index of different life forms, it was found that the βSOR of trees, shrubs and herbs were0.87, 0.95 and 0.94, respectively. ”Please recheck the Bray-Curtis distance index and βSOR.
9,“It was found that species compositional dissimilarityoftrees, shrubsand herbsin the study area both increased with distanceincreasing, indicating that there was an obvious species turnoverof plant community in Nanling Mountains.” “both ”is not proper here.
10,What is the “Predcited ecological distance”meaning in Fig.2?
11, In 3.2, it was said “Soil chemical propertieshad the highest explanation for β-diversity of trees, with the mean explanation rate of 52.5%,followed by herbs (40.3%) and shrubs (21.8%)”. However, I did not find the method of calculation in Methods;
12, In 3.3 “The relationships between β-diversity components of trees, shrubsand herbs and soil
chemical properties indifferent soil depthlayerswere calculatedusing the Person correlation and Mantel test.” This sentence should be moved to Methods;
13, For Table2 and 3 and 4, I wonder what the numbers in the data table mean. Slope of corelation? Or other parameters? Make it clear in the title;
Discusssion
14, To me, all the contents in 4.1 were results instead of discussion, as well as the most part of 4.3;
15, It was said in 3.2 that “Soil chemical properties had the highest explanation for beta diversity of trees, with explanation rate of 52.5%”. Then here in Discussion , you said “the soil element contents of 0-20 cm accounted for 63.5% of beta diversity of trees”. I don't understand why the 0-20 explanatory rate is greater than all the soil chemical properties;
Reference
16, All the references should be corrected,, including the abbreviation of the journals and capital and small letter;
17, Although I am not a native English speaker, I still see a lot of problems in English to be polished. Please check the full text thoroughly.
Author Response
Response for reviewer 1
This manuscript focused on the effects of soil the beta diversity patterns in Nanling Mountain, and found that soil chemical properties got great influence on beta diversity in this area, especially to the trees. The study is suitable for publication in Forests, however, I do not think this version is ready to be accepted. I have some comments and suggestions, listed as follows:
Introduction:
1,Accoring to the context, I think “continent and aquatic ecosystems” should be “terrestrial and aquatic ecosystems”;
Response：Thank you for your advice. As your suggestion, we have corrected this.
1,In paragraph 2, why not refer to the literature on beta diversity of legendre, et al 2009 on Ecology;
Response：Thank you for your advice. We referred the literature on beta diversity of legendre, et al 2013.
3,Change all the “fixed plot” to “dynamic plot”;
Response：Thank you for your advice. The study plots were set up in a fixed standard plot format and surveyed every 3 years, so we prefer to describe it as a fixed plot than dynamic plot.
Methods
4,In paragraph 1. “The study site was established in 2017 following CTFS standand census protocpls”. This sentence is wired to be here. Please move to the next paragraph;
Response：As your suggestion, we have corrected this.
5,I suggest to add a map of the plots locations so that we can just see where the sample locations are and the distance between them;
Response：As your suggestion, we have added the map of plot locations.
6,In “soil sampling and analysis”, the format “Lu Rukun,2000” should be modified;
Response：As your suggestion, we have corrected this.
7,Since there were 24 plots (including 21 forest plots and 3 mountain scrubby-meadow plots), Why the Bray-Curtis distance matrix were 18*18? And, I did not get the relationship between Bray-Curtis distance matrix and Sørensen dissimilarity index. If there was indeed no relationship between them, please move the Bray-Curtis distance matrix to the MS-GDM model paragraph;
Response：Thank you for your advice, we found this mistake. As your suggestion, we have moved the Bray-Curtis distance matrix.
Results
8,“By calculating the Bray-Curtis distance index of different life forms, it was found that the βSOR of trees, shrubs and herbs were0.87, 0.95 and 0.94, respectively. ”Please recheck the Bray-Curtis distance index and βSOR.
Response：Thank you for your advice. As your suggestion, we have corrected this mistake.
9,“It was found that species compositional dissimilarityoftrees, shrubsand herbsin the study area both increased with distanceincreasing, indicating that there was an obvious species turnoverof plant community in Nanling Mountains.” “both ”is not proper here.
Response：Thank you for your advice. As your suggestion, we have corrected this.
10,What is the “Predcited ecological distance”meaning in Fig.2?
Response：This plot indicates observed response data against the raw linear predictor (ecological distance) from the gdm model. And the predcited ecological distance was calculated automatically based on the coordinate data of latitude and longitude.
11, In 3.2, it was said “Soil chemical properties had the highest explanation for β-diversity of trees, with the mean explanation rate of 52.5%, followed by herbs (40.3%) and shrubs (21.8%)”. However, I did not find the method of calculation in Methods;
Response：The percent of deviance explained was also calculated automatically by gdm function “summary.gdm”.
12, In 3.3 “The relationships between β-diversity components of trees, shrubsand herbs and soil chemical properties indifferent soil depthlayerswere calculatedusing the Person correlation and Mantel test.” This sentence should be moved to Methods;
Response：Thank you for your advice. As your suggestion, we have corrected this.
13, For Table2 and 3 and 4, I wonder what the numbers in the data table mean. Slope of corelation? Or other parameters? Make it clear in the title;
Response：Thank you for your advice. As your suggestion, we have corrected this.
Discusssion
14, To me, all the contents in 4.1 were results instead of discussion, as well as the most part of 4.3;
Response：Thank you for your advice. As your suggestion, we have corrected these parts.
15, It was said in 3.2 that “Soil chemical properties had the highest explanation for beta diversity of trees, with explanation rate of 52.5%”. Then here in Discussion , you said “the soil element contents of 0-20 cm accounted for 63.5% of beta diversity of trees”. I don't understand why the 0-20 explanatory rate is greater than all the soil chemical properties;
Response：52.5% is the mean explanation rate of 4 soil depth of trees. And percent of explained deviance of 0-20 cm in Fig 1 is 63.5%.
Reference
16, All the references should be corrected, including the abbreviation of the journals and capital and small letter;
Response：Thank you for your advice. As your suggestion, we have corrected this.
17, Although I am not a native English speaker, I still see a lot of problems in English to be polished. Please check the full text thoroughly.
Response：Thank you for your advice. We have polished this manuscript.
Reviewer 2 Report
Thanks so much for inviting me to review the manuscript by Xu et al. The multi-point generalized dissimilarity model was used to analyze the influence of geographical distance, altitude and soil chemical properties of the four depth layers on the β-diversity patterns of different life forms, and the influence of environmental factors on β-diversity was quantified. The manuscript is well organized and the results are presented appropriately. However, there are many problems in the article, for example, the sample size is not clearly explained, the technical terms are not uniform, the scientific issues are not prominent, and the language description is inappropriate. In general, papers still need major revision.
Main comments:
1. Abstract: I recommend that authors rewrite the abstract to focus on the background objectives. Key findings and conclusions of the methodology. Please add a sentence explaining the necessity for research.
2. Introduction: Need to be more objective and quickly guide readers through the research goals and assumptions.
3. Discussion: The discussion is not in-depth and does not fully reflect the impact of soil depth on diversity. It is suggested to replace 4.2 and 4.3 with the relative contributions of dispersal limitation and environmental filtering, before discussing the impact of environmental factors on plant diversity.
4. Method: It is difficult for me to know how many soil samples you collected, how many quadrats you surveyed. It also doesn't mention how to measure your geographic distance. Is it suitable to choose a 2 m × 2 m plot for a shrub. Does the diversity calculation beta use multiple sites or pairwise diversity? I suggest using a paired beta diversity index to better explore patterns of variation in diversity.
Specific comments:
1. GDM is a good method to analyze the relationship between beta diversity of different plant life types and environmental factors, however, you did not mention the effect of geographical distance on beta diversity.
2. The results in Table 2-Table 4 show that soil factors have little correlation with plant diversity. Is it because the chosen method is inappropriate?
3. The standard error value should be added to Table 1, and the scale mark of the vertical axis should be added to Figure 3. Figure 4 is too blurry
4. This study aims to explore research under different soil depths. It is mentioned that different soil depths affect plant diversity through the root system. I suggest adding plant root data, which can better explain why plant diversity varies.
5. I suggest modifying the title. The current title does not better reflect the main idea of the article.
6. This paper discusses the stability based on different community types. However, the authors did not show the dominant species and community composition of different community types.
7. At the end of the paper, the authors should add a section summarizing the results.
8. Many English grammar questions. I recommend that authors find a native English speaker to improve their English expression skills.
The species composition of shrubs and herbaceous plants differed more than that of trees. Elevation is often significantly correlated with species diversity. like:
The β-diversity was decomposed into species turnover and species nesting components, and the species turnover component was dominant, which was consistent with the research results of subtropical forests.
This indicates that the environmental filtering process indicated by environmental factors such as altitude and soil, and the dispersal limitation characterized by geographical distance jointly affect the
β-diversity and composition of the Nanling mountainous plant community, which is consistent with the research results in other mountainous areas in the South.
9. Through the research on the Nanling forest ecosystem plots, it is found that the species composition of the Nanling mountain forest community is quite different (average βSOR0.92), and the plant community species composition is quite different. This sentence is very puzzling. You should specifically point out that the results of this study differ significantly from those of other studies.
10. Incorrect technical terms. Community building, decentralized restrictions.
11. With the increase of soil depth, the influence of soil elements on the β-diversity of trees, shrubs and herbaceous plants gradually decreased, which may be related to the change of plant root system with the increase of soil depth. What are the specific indicators of the root system?
Author Response
Thanks so much for inviting me to review the manuscript by Xu et al. The multi-point generalized dissimilarity model was used to analyze the influence of geographical distance, altitude and soil chemical properties of the four depth layers on the β-diversity patterns of different life forms, and the influence of environmental factors on β-diversity was quantified. The manuscript is well organized and the results are presented appropriately. However, there are many problems in the article, for example, the sample size is not clearly explained, the technical terms are not uniform, the scientific issues are not prominent, and the language description is inappropriate. In general, papers still need major revision.
Response：Thank you for your advice. We have done some revision.
Main comments:
1. Abstract: I recommend that authors rewrite the abstract to focus on the background objectives. Key findings and conclusions of the methodology. Please add a sentence explaining the necessity for research.
Response：Thank you for your advice. As your suggestion, we have corrected this.
2. Introduction: Need to be more objective and quickly guide readers through the research goals and assumptions.
Response：Thank you for your advice. As your suggestion, we have corrected some paragraph to be more objective.
3. Discussion: The discussion is not in-depth and does not fully reflect the impact of soil depth on diversity. It is suggested to replace 4.2 and 4.3 with the relative contributions of dispersal limitation and environmental filtering, before discussing the impact of environmental factors on plant diversity.
Response：Thank you for your advice. As your suggestion, we have adjusted 4.2 and 4.3.
4. Method: It is difficult for me to know how many soil samples you collected, how many quadrats you surveyed. It also doesn't mention how to measure your geographic distance. Is it suitable to choose a 2 m × 2 m plot for a shrub. Does the diversity calculation beta use multiple sites or pairwise diversity? I suggest using a paired beta diversity index to better explore patterns of variation in diversity.
Response：(1)We have 24 plots, each one has a 12 m× 15 m soil plot to get 1 soil sample of one depth layer, and this soil sample is a mixed sample composed of 8-10 samples of same soil depth. (2) Geographic distance was measured from latitude and longitude data of fixed plots. (3) Every tree plot had three 2 m × 2 m shrub plot. Although shrub plot area is less than 100 m2 , it still can illustrates shrub diversity patterns in the subtropical forest of Nanling. (4) The beta diversity was used is the Sørensen beta diversity, which was patitioned into the Simpson dissimilarity index and the nestedness dissimilarity.
Specific comments:
1. GDM is a good method to analyze the relationship between beta diversity of different plant life types and environmental factors, however, you did not mention the effect of geographical distance on beta diversity.
Response: Thank you for your advice. The environmental factors used in GDM have contained latitude and longitude data of fixed plots, and geographic distance was measured from that. The effect of geographical distance on beta diversity was showed in Fig 3 and 5.
2. The results in Table 2-Table 4 show that soil factors have little correlation with plant diversity. Is it because the chosen method is inappropriate?
Response：Thank you for your advice. Table 2-Table 4 show the positive or negative linear correlation between soil factors and plant diversity. The reason of the little correlation may be because the relationship between soil factors and plant diversity is nonlinear.
3. The standard error value should be added to Table 1, and the scale mark of the vertical axis should be added to Figure 3. Figure 4 is too blurry
Response：Thank you for your advice. We have corrected them.
4. This study aims to explore research under different soil depths. It is mentioned that different soil depths affect plant diversity through the root system. I suggest adding plant root data, which can better explain why plant diversity varies.
Response：Thank you for your advice. We haven’t collected plant root data of sample plot, so we only obtain the root distribution data from relevant papers. This will be considered and implemented in subsequent experiments.
5. I suggest modifying the title. The current title does not better reflect the main idea of the article.
Response：Thank you for your advice. We have corrected the title.
6. This paper discusses the stability based on different community types. However, the authors did not show the dominant species and community composition of different community types.
Response：Thank you for your advice. As your suggestion, we have added these information in Table S1.
7. At the end of the paper, the authors should add a section summarizing the results.
Response：Thank you for your advice. As your suggestion, we have added Conclusions.
8. Many English grammar questions. I recommend that authors find a native English speaker to improve their English expression skills.
The species composition of shrubs and herbaceous plants differed more than that of trees. Elevation is often significantly correlated with species diversity. like:
The β-diversity was decomposed into species turnover and species nesting components, and the species turnover component was dominant, which was consistent with the research results of subtropical forests.
This indicates that the environmental filtering process indicated by environmental factors such as altitude and soil, and the dispersal limitation characterized by geographical distance jointly affect the
β-diversity and composition of the Nanling mountainous plant community, which is consistent with the research results in other mountainous areas in the South.
Response：Thank you for your advice. As your suggestion, we have polished this manuscript.
9. Through the research on the Nanling forest ecosystem plots, it is found that the species composition of the Nanling mountain forest community is quite different (average βSOR0.92), and the plant community species composition is quite different. This sentence is very puzzling. You should specifically point out that the results of this study differ significantly from those of other studies.
Response：Thank you for your advice. As your suggestion, we have corrected this.
10. Incorrect technical terms. Community building, decentralized restrictions.
Response：Thank you for your advice. As your suggestion, we have corrected this.
11. With the increase of soil depth, the influence of soil elements on the β-diversity of trees, shrubs and herbaceous plants gradually decreased, which may be related to the change of plant root system with the increase of soil depth. What are the specific indicators of the root system?
Response：Thank you for your advice. We have corrected this to plant fine root amount.
Reviewer 3 Report
Comments and Suggestions for Authors
This article studied the effects of edaphic factors at different depths on β-diversity patterns for subtropical plant communities based on MS-GDM model in Southern China, which can provide scientific basis for the conservation of biodiversity and forest ecosystems in Nanling Mountains. The subject falls into the scope of Forests, but some questions need to be addressed as follows:
In this study, the authors have completed a large amount of research that is informative and interesting, but some parts are vague. For example, I can't see Figure 2 and Figure 4 clearly and suggest the author to provide high quality images.
In the discussion section of 4.3, some specific data appear abruptly, such as the explanation rate of the diffusion-limiting effect. This is not well represented in the previous results section, and I wish the authors would list specific figures in the contents and pictures of the results section.
Additionally, I think the authors could have made an opinion on the conservation of the diversity of local vegetation by conclusions section.
The format and details of this manuscript need to be carefully corrected, and since the line numbers are all incorrect, please refer to the annotated manuscript for some specific comments.
Author Response
Response for reviewer 3
This article studied the effects of edaphic factors at different depths on β-diversity patterns for subtropical plant communities based on MS-GDM model in Southern China, which can provide scientific basis for the conservation of biodiversity and forest ecosystems in Nanling Mountains. The subject falls into the scope of Forests, but some questions need to be addressed as follows:
In this study, the authors have completed a large amount of research that is informative and interesting, but some parts are vague. For example, I can't see Figure 2 and Figure 4 clearly and suggest the author to provide high quality images.
Response：Thank you for your advice. We have provided high quality images as attachments.
In the discussion section of 4.3, some specific data appear abruptly, such as the explanation rate of the diffusion-limiting effect. This is not well represented in the previous results section, and I wish the authors would list specific figures in the contents and pictures of the results section.
Response：Thank you for your advice. As your suggestion, we have corrected this.
Additionally, I think the authors could have made an opinion on the conservation of the diversity of local vegetation by conclusions section.
Response：Thank you for your advice. As your suggestion, we have added Conclusions.
The format and details of this manuscript need to be carefully corrected, and since the line numbers are all incorrect, please refer to the annotated manuscript for some specific comments.
Response：Thank you for your advice. As your suggestion, we have polished this manuscript.
Round 2
Reviewer 1 Report
Line 42，“are the core content” should be “are the core contents”;
Line 52, Usually we use “environment filtering”, not “environment filtration”;
Line 139, I have never heard of “fixed plots”. If you want to express you will continue to investigate this plot, you can use “permanent plots” or “dynamic plots”;
Line 223, “indicates” should be “indicate”;
The second paragraph of the Discussion was still a part of the Result.
Author Response
Line 42，“are the core content” should be “are the core contents”;
Response：Thank you for your advice. As your suggestion, we have corrected this.
Line 52, Usually we use “environment filtering”, not “environment filtration”;
Response：Thank you for your advice. As your suggestion, we have corrected this.
Line 139, I have never heard of “fixed plots”. If you want to express you will continue to investigate this plot, you can use “permanent plots” or “dynamic plots”;
Response：Thank you for your advice. As your suggestion, we have corrected this to “dynamic plots”.
Line 223, “indicates” should be “indicate”;
Response：Thank you for your advice. As your suggestion, we have corrected this mistake.
The second paragraph of the Discussion was still a part of the Result.
Response：Thank you for your advice. As your suggestion, we have corrected this paragraph.
Reviewer 2 Report
We think the manuscript has been sufficiently improved. This article is acceptable.
Author Response
We think the manuscript has been sufficiently improved. This article is acceptable.
Response：Thank you for your advice.
