Contrasting Effect of Thinning and Understory Removal on Soil Microbial Communities in a Subtropical Moso Bamboo Plantation
Sarah L. Addison
Round 1
Reviewer 1 Report
Contrasting effect of thinning and understory removal on soil microbial communities in a subtropical moso bamboo plantation.
This paper is interesting as it describes the differences found in the soil microbial community when both thinning, and/or understory removal are examined in relation to the soil physicochemical properties within a bamboo plantation over 3 time points. The science behind the manuscript is sound but the manuscript itself needs a bit of work as it can be quite difficult to read in places and some careful proofreading is necessary.
There are a number of sentences throughout the manuscript that don’t quite make sense eg. Line 31 (microbes act fundamental…), 34 (are generally sensitively respond…), 43 etc. The manuscript just needs a good read through to pick up these words throughout to make it easier for the reader. This will greatly improve the readability of the manuscript. I have not highlighted every single one as they are quite extensive throughout the document.
One thing that is lacking in the manuscript is the explanation of the changes in microbial community in respect to the productivity. It’s the really why does it matter? I’m not sure this is really explored in the manuscript and some careful thought to addressing this could make the manuscript more impactful. This is throughout the discussion and conclusions. The authors describe that the community shifts but not the real effects of what this shift means to the bamboo plantation. There feels like there’s something really missing tying it all together. This is just an observation but maybe something else to consider in the discussion is a bit around the use of sequencing and how this could expand the knowledge further as PLFA’s are very limited and subjective without possibly giving a true picture of community shifts.
Line 20: Maybe change this sentence around, the clearance causes the pH and water content to change which then results in microbial alterations. “Understory clearance decreased soil pH and soil water content resulting is increased soil fungal PLFAs and F:B ratio.”
Line 20: F:B – write in full with (F:B) as it’s the first time its introduced.
Line 55: AM fungi – write in full
Line 94: Ultisols – maybe a reference to the classification and what that type of soil means?
Lin 151: concents – contents
Table 1: what does AP stand for?
In the ANOVA for sampling time, there are 3 times compared, maybe within the supplementary material there could be the info for the pair-wise comparisons between each of the time points. Therefore, you might be able to show when the factors changes etc. It could be that some of these changes are due to seasonality rather than any other factors. Worth exploring as seasonality isn’t really discussed at all but could explain part of the variation as time is shown to be significant with a number of measurements reported.
Paragraph 3.2 Lines 172-184: The word ‘apparently’ is used throughout this paragraph. Consider being stronger in your definition, either there is a difference or this isn’t. It’s a very ambiguous word used in this context.
Table 2: Again, think about including the pair-wise comparisons across all time points.
Supplementary Table 1: it shows n = 3 but on all other tables it is n = 4. Please check?
Figure 3: this figure is good, but it would be helpful to have a supplementary table with the information behind this and in particular the variance numbers if this is possible.
Line 207: May be better to re-iterate your first hypothesis and then give why it was disproven, you don’t want the reader to have to go back and re-read what the hypothesis was. Also make it clear that you are comparing thinning etc to controls and that the total PLFAs have decreased relative to this. Make the comparisons clear with this paragraph otherwise you can’t say its due specifically to thinning. It currently reads a little ambiguously
Line 230-231: Attribute
Line 251: what do you mean by ‘activated’ and ‘deactivated’?
Line 255: re-iterate your 2nd hypothesis
Author Response
COMMENT 1: There are a number of sentences throughout the manuscript that don’t quite make sense eg. Line 31 (microbes act fundamental…), 34 (are generally sensitively respond…), 43 etc. The manuscript just needs a good read through to pick up these words throughout to make it easier for the reader. This will greatly improve the readability of the manuscript. I have not highlighted every single one as they are quite extensive throughout the document.
Response: We apologize for the poor language of our manuscript. We worked on the manuscript for a long time and the repeated addition and removal of sentence and sections obviously let to poor readability. We have now worked on both language and readability and have also involved native English speaker for language corrections. We really hope that the flow and language level have been substantially improved.We will be happy to edit the text further based on helpful comments from the reviewers.
COMMENT 2: One thing that is lacking in the manuscript is the explanation of the changes in microbial community in respect to the productivity. It’s the really why does it matter? I’m not sure this is really explored in the manuscript and some careful thought to addressing this could make the manuscript more impactful. This is throughout the discussion and conclusions. The authors describe that the community shifts but not the real effects of what this shift means to the bamboo plantation. There feels like there’s something really missing tying it all together. This is just an observation but maybe something else to consider in the discussion is a bit around the use of sequencing and how this could expand the knowledge further as PLFA’s are very limited and subjective without possibly giving a true picture of community shifts.
Response: Thanks for your comment. We added sentences to link the changes of soil microorganisms with litter decomposition rate according to our and other previous studies. Please refer to the details below.
Line 253-259: Considering that soil microorganism is the main driver of litter decomposition, and decreased soil fungal and bacterial biomass would suppress litter decomposition rate as previous studies revealed [1,2], our observations suggest that thinning exerts highly controls on soil nutrient availability (i.e. soil inorganic N concentration), which further inhibit soil microbial biomass, and consequently soil C cycling and forest productivity in this moso bamboo plantation.
Line 281-283: These findings propose that understory clearance changed soil pH and SWC, and consequently affect microbial biomass and community, and reduced litter decomposition rate as our published study reported in the present subtropical moso bamboo plantation [1].
COMMENT 3: Line 20: Maybe change this sentence around, the clearance causes the pH and water content to change which then results in microbial alterations. “Understory clearance decreased soil pH and soil water content resulting is increased soil fungal PLFAs and F:B ratio.”
Line 20: F:B – write in full with (F:B) as it’s the first time its introduced.
Line 55: AM fungi – write in full
Line 94: Ultisols – maybe a reference to the classification and what that type of soil means?
Lin 151: concents – contents
Response: Thanks for your comment. We have revised the manuscript as you suggested. Details were marked with red font in the revised version.
COMMENT 3：Table 1: what does AP stand for?In the ANOVA for sampling time, there are 3 times compared, maybe within the supplementary material there could be the info for the pair-wise comparisons between each of the time points. Therefore, you might be able to show when the factors changes etc. It could be that some of these changes are due to seasonality rather than any other factors. Worth exploring as seasonality isn’t really discussed at all but could explain part of the variation as time is shown to be significant with a number of measurements reported.
Response: AP stand for soil available phosphorus content.
As you suggest, we compared the average values of soil properties among different sampling event, and added statistical results to the supplementary Table 1.
We realize that our study region is within a typical subtropical monsoon climate, with distinct wet-hot and dry-cold seasons. Generally, over 83% and 66% of annual precipitation and radiation inputs to this region occur during the wet-hot season (From April to September). The temporal changes in soil properties could be ascribed to the changes in soil moisture, temperature, and other factors, as our previous studies explored, we mainly focus the treatment effect on soil properties in the present study.
COMMENT 4：Paragraph 3.2 Lines 172-184: The word ‘apparently’ is used throughout this paragraph. Consider being stronger in your definition, either there is a difference or this isn’t. It’s a very ambiguous word used in this context.
Response: We agree with the comment, and we use “significantly” to instead “apparently” in the revised version.
COMMENT 5: Table 2: Again, think about including the pair-wise comparisons across all time points.
Response: Thanks for your suggestion, however, we respectfully disagree the comment because the Table 2 contains the statistical results of the impact of sampling event on soil microbial community. Instead, we added pair-wise comparisons to the figure 3 in the revised version.
COMMENT 6:Supplementary Table 1: it shows n = 3 but on all other tables it is n = 4. Please check?
Response: We use “n=4” instead “n=3” in supplementary Table 1 in the revised version.
COMMENT 7: Figure 3: this figure is good, but it would be helpful to have a supplementary table with the information behind this and in particular the variance numbers if this is possible.
Response: Thanks for your suggestion, we added a table (supplementary table 2 in the revised version) with statistical significant and variance explained by the variables selected.
COMMENT 8:Line 207: May be better to re-iterate your first hypothesis and then give why it was disproven, you don’t want the reader to have to go back and re-read what the hypothesis was. Also make it clear that you are comparing thinning etc to controls and that the total PLFAs have decreased relative to this. Make the comparisons clear with this paragraph otherwise you can’t say its due specifically to thinning. It currently reads a little ambiguously
Response: Thanks for your comment. As you suggest, we re-iterated the hypothesis prior to discuss our inconsistent results in the revised version (marked with red font). Hopefully, the present version is more readability than before.
COMMENT 9: Line 230-231: Attribute
Response: Done
COMMENT 10: Line 251: what do you mean by ‘activated’ and ‘deactivated’?
Response: “activated” here means some group of bacteria are promoted in growth and activity, while “deactivated” means some group of bacteria are suppressed in growth and activity.
Line 255: re-iterate your 2nd hypothesis
Response: Thanks for your comment. As you suggest, the 2nd hypothesis was re-iterated in the revised version (marked with red font).
Reviewer 2 Report
I would like to thank the Editor for the opportunity to review the manuscript ,,Contrasting effect of thinning and understory removal on soil microbial communities in a subtropical moso bamboo plantation " Forests – 1919050
This manuscript is in line with the scope of the journal Forests. It touches on an interesting topic concerning the rather popular forest management methods of thinning and understory clearance on soil microbial properties. The paper was prepared in a manner typical of scientific papers. A correct division into chapters was used. The authors used correct analytical methods, but their presentation, especially in the form of tables, but also in the form of figures, should be improved to increase their understanding and readability. The cited literature is relatively new and fully relevant to the presented research. The paper is well written, correctly interpreted, and the results should be disseminated.
Detailed comments can be found below.
Introduction
Line 38-40 – The authors write , "Lots of previous studies....", and cite only two items of literature. In my opinion, this statement is incorrect to only two items of literature. Please provide more new literature items.
Line 38-40 – please briefly elaborate on your thoughts: ,"..... responses of soil microbial composition to forest management .....", please state what has already been studied and found.
Line 41-43- expand the thought what exactly is the impact?
Line 50-51 – expand on what indirect benefits the authors had in mind ?
Line 63-65 – "context-dependent," meaning on what specifically? What did the authors have in mind?
Line 75-79 - why is this type of bamboo so valuable and popular, add this information?
Materials and Methods
2.1. Field site and experimental design
I would suggest adding a map with the study area marked.
Line 94 - give more detailed characteristics of the soil (granulometric composition, basic parameters, e.g. C, N, pH)
2.3. Statistical analysis
Line 135 - state what test was used to check homogeneity and normality of variance
Line 136-140 - if the analysis of variance was ANOVA, please mention it in the methodology
Line 139 - what specific test are you referring to ? I think the abbreviation LSD is missing ?
Results
Table 1 - please provide explanations of abbreviations immediately after the abbreviation, e.g. SWC (%) - soil water content, etc.
Table 1 - I don't quite understand why the authors give one time here, when 3 terms were analyzed, and they refer to 3 levels of line 165? Were they averaged? How ? on what basis? Explain it further what the authors mean by the term time in this case?
Also, what is this effect, what unit is it expressed in? As you see this table needs to be replaced because it is incomprehensible? Why is there no combination of CK and TUR in it? What are the values given next to pH, for example?
Figure 1 - apply color to the graphs and correct the sizes of the graphs to increase readability. The order of the graphs should follow the order of analysis given in Table 1, that is, figure (a) - SWC, (b) -AP, (c) - NO3, (d)- NH4, (e) - TN, (f) - TP
Line 168-171 - change (3), (4), (5), (6) to (c), (d), (e), (f)
Table 2 - please provide the same explanation as in table 1. Moreover, how is the effect expressed here, in which unit?
Table 1 and 2 and Figure 1 and 2 - is ThxUR and TUR the same thing? if so, please standardize. if not, provide an explanation under the figures
Figure 2 - Apply color to the figures
Supplementary Material - Table 1- please indicate where the authors refer to the table from Supplementary Material? If it is given then they should also refer to it in the text? Also, its numbering to me is confusing
Discussion
Line 217-219 - expand on this thought. What kind of competition is involved here? Between what and what is this competition ? Also, what is this competition about ?
Line 238 - 241 - elaborate further on this thought. How do plants affect soil microorganisms? Did the authors mean plant secretions ? If so, please specify which ones and how they influence ?or the influence of physical and chemical conditions (e.g. humidity ....)
Author Response
COMMENT 1: I would like to thank the Editor for the opportunity to review the manuscript ,Contrasting effect of thinning and understory removal on soil microbial communities in a subtropical moso bamboo plantation " Forests – 1919050
This manuscript is in line with the scope of the journal Forests. It touches on an interesting topic concerning the rather popular forest management methods of thinning and understory clearance on soil microbial properties. The paper was prepared in a manner typical of scientific papers. A correct division into chapters was used. The authors used correct analytical methods, but their presentation, especially in the form of tables, but also in the form of figures, should be improved to increase their understanding and readability. The cited literature is relatively new and fully relevant to the presented research. The paper is well written, correctly interpreted, and the results should be disseminated.
Response: Thanks for your recognition of our work. The statements concerning the presentation, the forms of tables and figure have been corrected in the revised version.
COMMENT 2:Line 38-40 – The authors write , "Lots of previous studies....", and cite only two items of literature. In my opinion, this statement is incorrect to only two items of literature. Please provide more new literature items.
Response: We agree the comment, and we added more two related literature items in the revised version.
COMMENT 3: Line 38-40 – please briefly elaborate on your thoughts: ,"..... responses of soil microbial composition to forest management .....", please state what has already been studied and found.
Response:We added examples to the revised version to explore the mixed responses of soil microbial composition to forest management practice. Hopefully, the revised version is more readability than before. The details are as follows: For example, Wan et al. (2019) reported that understory removal significantly decreased soil fungal PLFA and the ratio of soil fungal to bacterial in subtropical Eucalyptus plantation. While, Lei et al (2021) explored that understory clearance increased soil fungal PLFA in a subtropical Chinese fir plantation.Clearly, more experimental studies are still needed to assess the response of soil microbial community to forest management practices.
COMMENT 4: Line 41-43- expand the thought what exactly is the impact?
Response: Combination effect between forest management practices could be facilitate, offset, and/or neutral. We added the exactly potential impact to the revised version. Details were marked with red font.
COMMENT 5: Line 50-51 – expand on what indirect benefits the authors had in mind ?
Response: Indirect benefits comes from the soil processes driven by soil microorganisms, such as soil carbon cycling, litter decomposition,etc.
COMMENT 6: Line 63-65 – "context-dependent," meaning on what specifically? What did the authors have in mind?
Response: “context-dependent” here means different study regions and forest types as many previous studies mentioned. We added specifically information to the revised version, hopefully it more readability than before.
COMMENT 7: Line 75-79 - why is this type of bamboo so valuable and popular, add this information?
Response: Moso bamboo having a fast growth rate, high productivity, short rotation time, and wide application. It make large contribution to meet people’s demand for wood. As you suggest, we added the information to the revised version.
COMMENT 8: I would suggest adding a map with the study area marked.
Response: We added a map for our field study area in the revised version (figure 1)
COMMENT 9:Line 94 - give more detailed characteristics of the soil (granulometric composition, basic parameters, e.g. C, N, pH)
Response: Detailed soil characteristics are shown in our supplementary table 1.
COMMENT 10: Line 135 - state what test was used to check homogeneity and normality of variance
Response: The homogeneity and normality of variance were test according to the formal normality test in SPSS. We added the method in statistical analysis section to the revised version.
COMMENT 11:Line 136-140 - if the analysis of variance was ANOVA, please mention it in the methodology
Response: Done
COMMENT 12:Line 139 - what specific test are you referring to ? I think the abbreviation LSD is missing ?
Response: “LSD” was added in the statistical analysis section of the revised version.
COMMENT 13:Table 1 - please provide explanations of abbreviations immediately after the abbreviation, e.g. SWC (%) - soil water content, etc.
Response: Done
COMMENT 14:Table 1 - I don't quite understand why the authors give one time here, when 3 terms were analyzed, and they refer to 3 levels of line 165? Were they averaged? How ? on what basis? Explain it further what the authors mean by the term time in this case?
Also, what is this effect, what unit is it expressed in? As you see this table needs to be replaced because it is incomprehensible? Why is there no combination of CK and TUR in it? What are the values given next to pH, for example?
Response: “Time” in table 1 is not one time , it stand for sampling time. Repeated measure ANOVA was used to analysis the sampling time and treatments effect on soil properties, and our results show that sampling time had significantly effect on soil properties except for soil pH, indicating that soil properties have seasonal dynamics.
TUR stand for the thinning with understory removal treatment, it can not combine wich CK treatment. Values in tables are statistical significance.
We added the explanation to the Table 1 in the revised version.
COMMENT 15:Figure 1 - apply color to the graphs and correct the sizes of the graphs to increase readability. The order of the graphs should follow the order of analysis given in Table 1, that is, figure (a) - SWC, (b) -AP, (c) - NO3, (d)- NH4, (e) - TN, (f) - TP
Response: Done as you suggest. We respectfully disagree to apply color to the graphs for the convenience of potential color blind readers. We rearranged the order of Table 1 to follow the order of the Figure 2 in the revised version.
COMMENT 16:Line 168-171 - change (3), (4), (5), (6) to (c), (d), (e), (f)
Response: Done
COMMENT 17:Table 2 - please provide the same explanation as in table 1. Moreover, how is the effect expressed here, in which unit?
Response: Values in tables are statistical significance. We added the explanation to the Table 2 in the revised version.
COMMENT 18:Table 1 and 2 and Figure 1 and 2 - is ThxUR and TUR the same thing? if so, please standardize. if not, provide an explanation under the figures
Response: Th×UR stand for the interactive effect between the Thinning and the understory removal treatment, while TUR stand for the treatment of thinning with understory removal.
COMMENT 19: Figure 2 - Apply color to the figures
Supplementary Material - Table 1- please indicate where the authors refer to the table from Supplementary Material? If it is given then they should also refer to it in the text? Also, its numbering to me is confusing
Response: We respectfully disagree to apply color to the graphs for the convenience of potential color blind readers.
The supplementary table was cited in the discussion section (Line 253 and 292 in the revised version)
COMMENT 20: Line 217-219 - expand on this thought. What kind of competition is involved here? Between what and what is this competition ? Also, what is this competition about ?
Response: The treatment of thinning reduced the competition between removed trees and remain trees for soil water and nutrients.
COMMENT 21: Line 238 - 241 - elaborate further on this thought. How do plants affect soil microorganisms? Did the authors mean plant secretions ? If so, please specify which ones and how they influence ?or the influence of physical and chemical conditions (e.g. humidity ....)
Response: Plants provide carbon resource and nutrient substrate through root exudation and dead residue for life activities of soil microorganism, and it is generally accepted that soil microbial community is controlled by the bottom-up force.
