Composition of Soil Bacterial and Nematode Communities within Soil Aggregates in a Kiwifruit Orchard under Cover Crop Treatment
Round 1
Reviewer 1 Report
In this study, a field experiment in a kiwifruit orchard with cover crops was conducted to estimate the distribution of soil bacteria and nematodes with different soil aggregate sizes, and micro-aggregate and cover crop treatments. The experimental design is well performed,the research work and analysis results show some interesting conclusions.I see the potential of research, but there are still some issues that need to be addressed. I hope that my comments will help improve the quality of the manuscript.
Line 16，Delete the word ‘crop’ that is repeated.
Line271：as well as
Line328， ‘s’ needs to delete.
Line347：’wad’ needs to be revised
Line377:’abundance’ needs to be revised
Line380:’increased’ maybe need to be revised
Line382：its 3.2
Line389:’because of their large sized body’… this explanation needs to be a little more specific
Line391-394：This sentence needs to be a little more concise.
Line396-397: This sentence needs to be revised.
Author Response
Point 1: Line 15 and 16: Delete the word ‘crop’ that is repeated.
Response 1: Thanks for your advice. We have deleted the word ‘crop’ and replace it with ‘cover’ in Line15 and 16 in the manuscript.
Point 2: Line249: as well as.
Response 2: Thanks for your advice. We have changed ‘and’ to ‘as well as’ in Line 249 in the manuscript.
Point 3: Line307: ‘s’ needs to delete.
Response 3: Thanks for your advice. We have deleted the ‘s’ in Line 307 in the manuscript.
Point 4: Line336: ‘wad’ needs to be revised.
Response 4: Thanks for pointing this out. We have changed ‘wad’ to ‘was’ in Line 336 in the manuscript.
Point 5: Line342: ‘abundance’ needs to be revised.
Response 5: Thanks for your advice. We have revised the ‘abundance’ to ‘relative abundances’ in Line 342 in the manuscript.
Point 6: Line363: ‘increased’ maybe need to be revised
Response 6: Thanks for your advice. We have revised ‘increased’ to ‘increasing’ in Line 363 in the manuscript
Point 7: Line365: its 4.2
Response 7: Thanks for pointing this out. We have changed ‘4.1’ to ‘4.2’ in Line 365.
Point 8: Line374: ‘because of their large sized body’… this explanation needs to be a little more specific. And Line378-382：This sentence needs to be a little more concise.
Response 8: Thanks for your advice. We have added the more specific explanation about ‘because of their large sized body’, and reorganized the sentence in Lin 373-376.
Author Response File: 
Author Response.doc
Reviewer 2 Report
Overall, this is an interesting study conducted by Li et al., to study the composition of soil bacterial and nematode communities within soil aggregates in a kiwifruit orchard under cover crop treatment. I think the research question is interesting. However, the way the results are discussed in the manuscript needs minor rework. I hope the authors find these comments and suggestions helpful. I suggest manor revisions before this manuscript is acceptable for publication. I have clearly indicated all my opinions and suggestions below.
Minor Comments:
What is the hypothesis of your research?
Section 2.4: Which variable regions were targeted for 16S sequencing.
Line 232-234: This is not obvious from the relative abundance figure. Were they statistically significant differences?
Line 306: What correlation analysis was performed for table S7?
Line 354-356: Please validate this statement with reference. What nutrient deficiency are you talking about?
Author Response
Point 1: What is the hypothesis of your research?
Response 1: Thanks for your advice. Exploring the distribution characteristics of soil nematodes and microbes in different sized aggregates under soil management practices contribute to supplement our understanding of the dynamics of soil food web and enhance the effectiveness of soil management practices. We hypothesized that cover crop will have strong effects on both bacterial and nematode communities in aggregates levels, and there are significant associations between bacterial and nematode communities.
Point 2: Section 2.4: Which variable regions were targeted for 16S sequencing.
Response 2: Thanks for pointing this out. In this study, V4 region were targeted for 16S sequencing, and we have added this in the manuscript.
Point 3: Line 240-242: This is not obvious from the relative abundance figure. Were they statistically significant differences?
Response 3: Thanks for pointing this out. Figure 1A just shows the relative abundance of the top 10 species at phylum level, while the permutational multivariate analysis of variance (PERMAVONA) conducted on the entire bacterial community. So, the results of Figure 1A and PERMANOVA results do not conflict.
Point 4: Line 292: What correlation analysis was performed for table S7?
Response 4: Thanks for your advice. Table S7 is the results of redundancy analysis (RDA) of bacterial and nematode community changes with soil chemical factors. And from Table S7 we can see that bacterial community is mainly affected by SOC and TN, while nematode community is mainly affected by SOC and C/N.
Point 5: Line 342-344: Please validate this statement with reference. What nutrient deficiency are you talking about?
Response 5: Thanks for your advice. In Line 337-342, we have cited references to explain the reason of the distribution of copiotrophs (e.g., Chloroflexi and Acidobacteriota) and oligotrophs (e.g., Bacteroidota) in different soil sized aggregates. Because of the low soil nutrients in Mega- and macro- aggregates, so the copiotrophs bacteria (e.g., Chloroflexi and Acidobacteriota) was enriched. While the micro- aggregate has high soil nutrients that promote the oligotrophs (e.g., Bacteroidota) enriched.
Author Response File: Author Response.doc
Reviewer 3 Report
The manuscript agronomy-2323861," Composition of soil bacterial and nematode communities within soil aggregates in a kiwifruit orchard under cover crop treatment", studied the effect of aggregates with different sizes under cover crop treatment and clean tillage on the composition of bacterial and nematode communities in a kiwifruit orchard. I consider that the study has the potential for publication in the Agronomy journal. However, the manuscript needs to improve the presentation of the results and conclude based on the study limitations. Therefore, I consider that the work needs improvement for publication in the Agronomy journal.
General comments:
1. The study presents the results of one experiment, using one collect and three replicates. To guarantee solid results (avoid causality) is necessary to establish the experiment in another location and/or perform two collects on time. This is the main lack of the present study.
2. The conclusions should be focused on before mentioned limitation.
3. I suggest analyzing the sequence data using QIIMe2. Please, you should present the rarefaction curves.
4. Figure 3 could be omitted. The C/N is a covariate of SOC and TN parameters.
Specific comments are in the attached file.
Comments for author File: 
Comments.pdf
Author Response
Point 1: The study presents the results of one experiment, using one collect and three replicates. To guarantee solid results (avoid causality) is necessary to establish the experiment in another location and/or perform two collects on time. This is the main lack of the present study.
Response 1: Thanks for your advice. In future studies, we will perform more than two collects on time for comprehensively analyze the regulation mechanisms of soil properties on soil microbial and nematode community within different sized aggregates.
Point 2: The conclusions should be focused on before mentioned limitation.
Response 2: Thanks for your advice. We have revised the conclusions of the study in the manuscript.
Point 3: I suggest analyzing the sequence data using QIIMe2. Please, you should present the rarefaction curves.
Response 3: Thanks for your advice. In this study, we analyzed the sequence data using QIIME, because of our negligence a writing error occurred, and we have change in the manuscript. In addition, we have added the rarefaction curves in the Supplementary information Fig S1.
Point 4: Figure 3 could be omitted. The C/N is a covariate of SOC and TN parameters.
Response 4: Thanks for your advice. But we think C/N is an indicator of soil chemistry, which influence soil microbial and nematode community.
Point 5: I suggest you to use different color to difference between CC and CK in figure 1B, figure 2B and figure 3.
Response 5: Thanks for your advice. We have used different color to difference between CC and CK in figure 1B, figure 2B and figure 3 in the manuscript.
Point 6: Line: 233, why ‘mega-aggregates’ and ‘macro-aggregates’ defined as ‘LMA’ and ‘SMA’?
Response 6: Thanks for pointing this out. In this study, three aggregate fractions include mega-aggregates (>2 mm), macro-aggregates (0.25–2 mm) and micro-aggregates (<0.25 mm) according to Trivedi et al, 2017 (Soil aggregation and associated microbial communities modify the impact of agricultural management on carbon content). Mega-aggregates (>2 mm) are the large microaggregates, so we defined abbreviations as LMA; macro-aggregates (0.25–2 mm) are the small macroaggregates, so we defined abbreviations as SMA.
Point 7: Line 413-415: Limitations and Perspective.
Response 7: Thanks for your advice. We have described the limitations and perspective of the study in Line 417-421.
Author Response File: Author Response.doc
