Soil Depth Determines the Composition and Diversity of Bacterial and Archaeal Communities in a Poplar Plantation
Round 1
Reviewer 1 Report
The present study indicated that soil depth affects the complexity and diversity of microbial community in a poplar plantation. It is a very comprehensive work and exhaustive study was done by the authors.
In my opinion:
-manuscript fit very well into the scope of the journal and presents
very hot and important topic concerning belowgroung microorganisms
-abstract is informative
-whole manuscript is very interesting and very important to understand
belowground microbial diversity under poplar plantation
-results are presented in appropriate clear way
-In my opinion this manuscript is a very good introduction into the
topic and all manuscript is in accordance with issues important for
forest managers or scientists, underlining the relevant role and changes
of microorganisms in depths and also focusing on relationship between
bacterial and archaeal community compositions and edaphic factors which
is very relevant from the practic point of vieu.
Author Response
Point 1: The present study indicated that soil depth affects the complexity and diversity of microbial community in a poplar plantation. It is a very comprehensive work and exhaustive study was done by the authors.
Response 1: Thanks for the positive comments.
Point 2: manuscript fit very well into the scope of the journal and presents very hot and important topic concerning belowground microorganisms
-abstract is informative
-whole manuscript is very interesting and very important to understand belowground microbial diversity under poplar plantation
-results are presented in appropriate clear way
Response 2: Thanks for the positive comments.
Point 3 -In my opinion this manuscript is a very good introduction into the topic and all manuscript is in accordance with issues important for forest managers or scientists, underlining the relevant role and changes of microorganisms in depths and also focusing on relationship between bacterial and archaeal community compositions and edaphic factors which is very relevant from the practic point of view.
Response 3: Thanks for the positive comments.
Reviewer 2 Report
Title: Soil depth determines the composition and diversity of bacterial and archaeal communities in a poplar plantation.
Author: Huili Feng et al.
General Comments
The manuscript describes the vertical distributions of bacterial and archaeal abundance and richness in poplar plantation soils. The article is undoubtedly interesting and crucial for understanding of below ground microbial functioning under forest planting ecosystems and the manuscript is perfectly fit with the scope of forests. Although the manuscript showed some interesting results and data analyses are systematic and informative, I found two anomalies. Firstly, the objectives- hypotheses mentioned in abstract and in introduction need to be consistence according to the background information given in introduction. Secondly to test the hypotheses you need to compare your findings with the natural forest, adjacent to your plantations (i.e. same climatic and edaphic conditions). The main limitation of the study is not to include the natural forest/or undisturbed adjacent land in the study. These two and few other minor comments (as specified below) need to address. Overall, I am positive about the manuscript, however the manuscript can be recommended to publish after resolving these two issues and other minor corrections.
Major comments:
In the abstract the object is ‘ Potential effect on the biogeochemical cycle such as methane’ (Line 18-19) but in the end of introduction (Line 62-69) this objective was not included. In fact, in the analytical or experimental parts of the study methane was not included. So please make consistent between abstract-introduction.
The hypotheses were set to compare soil microbes between natural and plantation forests but in reality natural forest was not included in the experiment. So the hypotheses need to rewrite on the basis of experiments and analyses that have been done. In one hypothesis transition zone of microbes predicted to be deeper in plantation forest (Line 67) but in introduction this issue was not discussed. The ground of each hypotheses must be reviewed in introduction section.
Figure’s captions are need to rewrite as self-explanatory (explain in details) and need modifications as suggested.
Minor comments
Line 29-32 ‘ … and showed that subsurface soil……..compared with surface soil’ this is too much speculative statement . No biogeochemical process has been studied. So please rewrite the concluding remark based on your findings.
Line 40 should be ….restricted to the surface soil [ ]- please add ‘soil’.
Line 43 … ‘plantation greenhouse gas emissions’ please revise the sentence.
Line 76 The soil is Gleysols [ ] not ‘Gleysol soil’.
Line 92 not ‘ring cutter’ using a ring core (diameter….).
Line 93 not ‘Ziplock bags’ resalable plastic bags.
Line 96 sieved through 2 mm mesh (not filters).
Line 101 Soil organic C (SOC) was determined by…… not’ surveyed with’
102-107 Please try to use reference for methods.
Please include the methods of diversity index, alpha & beta patters etc. in Materials and Methods section.
Tables and Figures
Captions of Figure 2 and 3 need more explanation. Please explain in details of these figures (lines 172 and 190)
Figure 4 & 5 these two figures are difficult to understand. To make it easy please divide each figure into two panels a. bacteria and b. archaea . Please try include all <2% relative abundance in ‘others’. The percentages inside the brackets ……. Please delete of and in.
Figure 6 Need detailed caption. I can’t see any percentage inside brackets. (?)
Figure 7 The caption is not matching with the figure (may be by mistake). I would suggest a simple table for Pearson’s correlation matrix. Color expression of correlation coefficient is not a good idea.
English language is mostly OK. If possible reading the manuscript by a qualified person would be fine.
Author Response
Point 1: The manuscript describes the vertical distributions of bacterial and archaeal abundance and richness in poplar plantation soils. The article is undoubtedly interesting and crucial for understanding of below ground microbial functioning under forest planting ecosystems and the manuscript is perfectly fit with the scope of forests. Although the manuscript showed some interesting results and data analyses are systematic and informative, I found two anomalies. Firstly, the objectives- hypotheses mentioned in abstract and in introduction need to be consistence according to the background information given in introduction. Secondly to test the hypotheses you need to compare your findings with the natural forest, adjacent to your plantations (i.e. same climatic and edaphic conditions). The main limitation of the study is not to include the natural forest/or undisturbed adjacent land in the study. These two and few other minor comments (as specified below) need to address. Overall, I am positive about the manuscript, however the manuscript can be recommended to publish after resolving these two issues and other minor corrections.
Response 1: We thank the reviewer for the constructive suggestions. We modified the objective mentioned in the abstract to make it consistence with the hypothesis mentioned in introduction. Please see lines 18-19. We also revised the hypotheses mentioned in introduction based on what we actually do in this study. Please see lines 69-71. In the study area, it is nearly impossible to find natural forests, as most lands were used as agricultural land. Therefore, we initially want to compare with other similar studies for the natural forest soils, which is not quite reasonable and persuasive.
Point 2: In the abstract the object is ‘Potential effect on the biogeochemical cycle such as methane’ (Line 18-19) but in the end of introduction (Line 62-69) this objective was not included. In fact, in the analytical or experimental parts of the study methane was not included. So please make consistent between abstract-introduction.
Response 2: We removed the sentence in the abstract and modified our hypotheses. Please see lines 18-20 and lines 69-74.
Point 3: The hypotheses were set to compare soil microbes between natural and plantation forests but in reality natural forest was not included in the experiment. So the hypotheses need to rewrite on the basis of experiments and analyses that have been done. In one hypothesis transition zone of microbes predicted to be deeper in plantation forest (Line 67) but in introduction this issue was not discussed. The ground of each hypotheses must be reviewed in introduction section.
Response 3: We followed the reviewer’s comments and modified the hypotheses in the introduction based on what we actually did in the study. Please see lines 69-74.
Point 4: Figure’s captions are need to rewrite as self-explanatory (explain in details) and need modifications as suggested.
Response 4: We revised the captions of Figure 2, 3, 4, 5, 6 for self-explanatory as suggested. Please see lines 182-187, 205-210, 214-217, 221-224, 238-245.
Point 5: Line 29-32 ‘ … and showed that subsurface soil……..compared with surface soil’ this is too much speculative statement . No biogeochemical process has been studied. So please rewrite the concluding remark based on your findings.
Response 5: We rewrote the concluding remark based on what we did in this study. Please see lines 31-34.
Point 6: Line 40 should be ….restricted to the surface soil [ ]- please add ‘soil’.
Response 6: Done as suggested. Please see line 43.
Point 7: Line 43 … ‘plantation greenhouse gas emissions’ please revise the sentence.
Response 7: Done as suggested. Please see line 46.
Point 8: Line 76 The soil is Gleysols [ ] not ‘Gleysol soil’.
Response 8: Done as suggested. Please see line 81.
Point 9: Line 92 not ‘ring cutter’ using a ring core (diameter….).
Response 9: Done as suggested. Please see lines 97-98.
Point 10: Line 93 not ‘Ziplock bags’ resalable plastic bags.
Response 10: Done as suggested. Please see line 99.
Point 11: Line 96 sieved through 2 mm mesh (not filters).
Response 11: Done as suggested. Please see line 102.
Point 12: Line 101 Soil organic C (SOC) was determined by…… not’ surveyed with’
Response 12: Done as suggested. Please see line 106.
Point 13: 102-107 Please try to use reference for methods.
Response 13: We added some related reference for soil physiochemical characteristics. Please see lines 109, 112 and corresponding reference in lines 410.
Point 14: Please include the methods of diversity index, alpha & beta patters etc. in Materials and Methods section.
Response 14: Done as suggested. Please see lines 145-150.
Point 15: Captions of Figure 2 and 3 need more explanation. Please explain in details of these figures (lines 172 and 190).
Response 15: Done as suggested. Please see lines 182-187 and 205-210.
Point 16: Figure 4 & 5 these two figures are difficult to understand. To make it easy please divide each figure into two panels a. bacteria and b. archaea . Please try include all <2% relative abundance in ‘others’. The percentages inside the brackets ……. Please delete of and in.
Response 16: Done as suggested. Please see lines 211-217 and 218-224.
Point 17: Figure 6 Need detailed caption. I can’t see any percentage inside brackets. (?)
Response 17: Done as suggested. Please see lines 239-245.
Point 18: Figure 7 The caption is not matching with the figure (may be by mistake). I would suggest a simple table for Pearson’s correlation matrix. Color expression of correlation coefficient is not a good idea.
Response 18: Yes, we made a mistake. Done as suggested. Please see lines 246-252.
Author Response File: 
Author Response.docx
Round 2
Reviewer 2 Report
Title: Soil depth determines the composition and diversity of bacterial and archaeal communities in a poplar plantation.
Author: Huili Feng et al.
After 1st round review, although the quality of manuscript has been improved and most of the comments have been addressed correctly, three issues still remain unsolved.
1. We commented on concluding statement of Abstract (Line 28-31) that it should be based on findings of the study. It says “Those bacteria and archaea distributing soil profiles would be crucial to indicate biogeochemical processes of the forest ecosystem”. Again this was not finding of the experiments, no biogeochemical process was tested in the study. Look, you have 3 major findings 1) Soil physicochemical properties changed with depths and some are correlated with microbial abundance/ diversity, 2) Diversity of microbes decreased with depth, 3) The relative abundance some microbes vary with depth. You should make a concluding statement covering these 3 findings.
2. In the Materials and Methods we commented to include methods of diversity index, ACE (coverage estimation) and Chao1 (i. e how you calculate these- by which formula or equations etc), but was not included. Please include these in materials and methods.
3. You split up Figure 4 & 5 (Thanks!), now you can see for archaea (also many bacteria), phyla and class level abundance values (%) are same and so what is the justification of showing two steps of classification system (phyla and class). My suggestion is please remove the phyla level figure (Figure 4) and keep only figure 5 ((a) Bacterial class and (b) Archaea class, and also please correct Y axis as ‘Community abundance (%)’ )
Minor:
(Line 62 …..the objectives were, because you have three objectives)
Author Response
Point 1: We commented on concluding statement of Abstract (Line 28-31) that it should be based on findings of the study. It says “Those bacteria and archaea distributing soil profiles would be crucial to indicate biogeochemical processes of the forest ecosystem”. Again this was not finding of the experiments, no biogeochemical process was tested in the study. Look, you have 3 major findings 1) Soil physicochemical properties changed with depths and some are correlated with microbial abundance/ diversity, 2) Diversity of microbes decreased with depth, 3) The relative abundance some microbes vary with depth. You should make a concluding statement covering these 3 findings.
Response 1: We deleted the sentences related to the biogeochemical processes that haven’t been involved in this study in the abstract. Please see lines 31-32. The three major findings were presented in the abstract. Also, we rephrased the concluding remarks in lines 358-365.
Point 2: In the Materials and Methods we commented to include methods of diversity index, ACE (coverage estimation) and Chao1 (i. e how you calculate these- by which formula or equations etc), but was not included. Please include these in materials and methods.
Response 2: We may misunderstand the comments in the first round revision. At this version, we added the formula for Shannon, Chao1, and Coverage indexes and their references. Please see lines 144-153.
Point 3: You split up Figure 4 & 5 (Thanks!), now you can see for archaea (also many bacteria), phyla and class level abundance values (%) are same and so what is the justification of showing two steps of classification system (phyla and class). My suggestion is please remove the phyla level figure (Figure 4) and keep only figure 5 ((a) Bacterial class and (b) Archaea class, and also please correct Y axis as ‘Community abundance (%)’ )
Response 3: Thank you for your advice. We did as suggest and we also think that the relative abundance of microbe at the phyla level is worth to present in the supplementary.
Point 4: (Line 62 …..the objectives were, because you have three objectives)
Response 4: Done. Please see line 65.
