Effect of Mycorrhizal Inoculation and Irrigation on Biological Properties of Sweet Pepper Rhizosphere in Organic Field Cultivation

Round 1

Reviewer 1 Report

This experiment deals with the improvement of quality and quantity of sweet pepper production. All relevant scientific preliminaries were provided, the methods were adequately described.

The results are clearly presented, with good conclusions. All tables and graphs are clear, understandable and necessary. The overall quality of the presentation is good. The references are sufficient and necessary.

Several similar investigations have been carried out recently, dealing with different cultivated plants, so the novelty of the present work is average. Besides, the interest to the readers seems to be high, because of the well selected plant, the sweet pepper. In my opinion this work can be useful for pepper producers to select the appropriate method of cultivation in their particular field conditions.

I don't feel qualified to review the English used by the authors but I understood well all the text. I haven't found any mistakes.

Author Response

Review 1 - accept

Thank you very much for your review.

Author Response File: Author Response.pdf

Reviewer 2 Report

Jamiołkowska et al. present their results on the impact that inoculation with arbuscular mycorrhizal fungi and irrigation has on the rhizosphere of sweet pepper rhizosphere in an organic field setting. Their experimental design and controls were appropriate for evaluating the parameters they measured. Specifically, they looked at soil catalase activity, culturable microbial populations, the density of identified fungal species, fungal metagenome comparisons between treatments, and carbon utilization patterns of at microbial suspensions using Biolog EcoPlates. However, the presentation of the results is not very professional and must be improved. They were able to draw interesting conclusions, but do not sufficiently highlight these throughout the manuscript, nor do they sufficiently describe how their findings connect with the broader published literature. Below are major and minor comments that need to be addressed before this manuscript can be considered further for publication.

Major comments:

1. Some methods are not sufficiently described (various points are discussed in the minor comments below). If text length is not limited, all methods need to be described with sufficient detail to allow another scientist skilled in this area of research to replicate the results.
2. Overall, the figures simply are not publication ready. As outlined in the minor comments below, there are things that need to be adjusted for nearly every figure. Furthermore, the authors should seek to have a consistent format across figures to ensure that the reader can fully follow their description of the results from beginning to end.
3. In its current format, the manuscript is purely descriptive, and in the Results section, no summative statements are provided for each sub-section that briefly summarize the key findings. For the authors to make this manuscript relevant to the reader, they need to rectify this and ensure that the meaning of each significant result is put in context. In addition, the results section should flow easily, with one result setting the stage for describing the next.
4. Similarly, with the Discussion, there is no clear direction in linking the results of this study to those of already published research. The authors need to thoroughly consider their findings in the broader context of the published literature and specify what they have contributed with this study. In its present format, the authors only indicate that they have partially verified what is already known. However, with a bit more effort, I think they could show that they have novel information to contribute.

Minor comments:

1. In the abstract, the authors do not properly define the type of mycorrhizal fungi they used for this study. They need to indicate that they used arbuscular mycorrhizal fungi as there are many different types of mycorrhizal fungi, including orchid, ericoid, ecto-, and even endecto-mycorrhizal fungi.
2. The authors use the acronym “P” for control plants early in the abstract, but then define the acronym two more times within the same paragraph. It only needs to be defined once and then used properly from that time forward.
3. Line 38: the term “specific biological activity” is very broad and vague. Please be more specific in explaining what you mean by this term.
4. Line 64: replace “also” with “including”
5. Line 67: Although the claim in this sentence may be true, please provide a justification (e.g., quantify how much is produced worldwide and then cite a reliable reference).
6. Line 68: The term “severe” is generic. Please be more specific and provide references to support your claims.
7. Lines 83-84: Describing the plants as the “object” of the study is unusual. You can simply state that “The sweet pepper (species name) hybrid ‘Roberta F1’, a Polish cultivar important for commercial production, was used in this study.
8. Line 88: When listing a plant type, you need to include the species name as well, not just the common name.
9. Line 91: What was the timing (e.g., time points or developmental stages) when Bio-Algeen was applied?
10. Line 125: please explain what you mean by dilution ranges and how they were prepared.
11. Line 147: Change vortex to vortexed
12. Line 161-162: Delete “were done”.
13. Line 162-163: What program did you use to prepare the PCA plots?
14. Line 163-165: This sentence is confusing. Please re-write with greater clarity.
15. Line 165: How did you generate the heatmap?
16. Line 179: Delete “The analysis of the results of the 3-year study showed that…”
17. Table 1: The spacing is not consistent for the letters next to the experimental values that indicate statistical significance. Please fix.
18. Line 190: Could you please provide a brief summary sentence at the end of this paragraph briefly explaining the significance of the stated results? The same comment holds for all other paragraphs in the results section. Simply stating the results in a descriptive manner does not help the reader understand the biological significance of the finding. Your role as the writer is to provide your interpretation briefly in the results section and in detail later in the discussion.
19. Lines 229-231: This is a perfect example of what each results paragraph, or at least each results section, should include as indicated in the previous comment.
20. Figure 1: The caption for the figure should describe the meaning of the colored boxes in the figure. Furthermore, for the results displayed in this figure, shouldn’t there be some statistical analysis performed to evaluate whether the abundance of one fungal species in one treatment is significant compared to another treatment?
21. Figure 2: At 100% zoom, the text on the graph is very difficult to read. It needs to be enlarged and the size of the graphs reduced so all three panels can fit on one page.
22. Figure 3: The same comment as with figure 2 regarding text size, but also decimals (“.”) should be used instead of commas (“,”) on the y-axis labels.
23. Line 298: change “confirm” to “confirmed”
24. Line 300: change “in the case” to “for”
25. Figure 4: The arrangement of this figure is very unprofessional, making it very difficult to interpret. Please improve (e.g., at least make sure the y-axis caption doesn’t cover the numbers!)
26. Figure 6: Please fix the axis labels, which have “,” as a decimal instead of “.”
27. Line 339: The manuscript you cite for this sentence uses a phrase that is very understandable: “the biotic component of soil quality.” Instead of saying “biological component of the soil”, use the same phrase as the manuscript your citing. It is much clearer.
28. The Conclusion section is fairly well written and provides some of what I felt was missing in the Results and Discussion sections. The authors should highlight these conclusions in the body of the text more prominently so that the same points in the conclusion are clearly supported in the mind of the reader.

Author Response

Review 2

Major comments:

1. Some methods are not sufficiently described (various points are discussed in the minor comments below). If text length is not limited, all methods need to be described with sufficient detail to allow another scientist skilled in this area of research to replicate the results.

Very detailed description of the research methods the reader will find in the references given for each method. I believe that detailed description of methods should be avoided, because many specialists know them or they can see the reference. Long description of the methods makes the article longer, and the methodology is longer than the description of the results. In my opinion should not be the case.

1. Overall, the figures simply are not publication ready. As outlined in the minor comments below, there are things that need to be adjusted for nearly every figure. Furthermore, the authors should seek to have a consistent format across figures to ensure that the reader can fully follow their description of the results from beginning to end.

As described in the minor comments below, the figures were adjusted according to the comments of the reviewer. 

3. In its current format, the manuscript is purely descriptive, and in the Results section, no summative statements are provided for each sub-section that briefly summarize the key findings. For the authors to make this manuscript relevant to the reader, they need to rectify this and ensure that the meaning of each significant result is put in context. In addition, the results section should flow easily, with one result setting the stage for describing the next.

In the manuscript (Results section), short summaries to each sub-section have been added as suggested by the reviewer.

Minor comments:

1.In the abstract, the authors do not properly define the type of mycorrhizal fungi they used for this study. They need to indicate that they used arbuscular mycorrhizal fungi as there are many different types of mycorrhizal fungi, including orchid, ericoid, ecto-, and even endecto-mycorrhizal fungi.

In my opinion, it should not be written in the abstract that arbuscular mycorrhizal fungi were used, because the root colonization of these fungi was not studied and the number of arbuscules formed by them was not studied. So it is better to use the general term "mycorrhiza mushrooms (MF)", which is practiced today in the world of science. Moreover, most researchers of the subject know that the genera Rhizophagus, Gigaspora or Claroideoglomus are arbuscular mycorrhizal fungi.

2.The authors use the acronym “P” for control plants early in the abstract, but then define the acronym two more times within the same paragraph. It only needs to be defined once and then used properly from that time forward.

This has been corrected according the reviewer's comments.

Line 38: the term “specific biological activity” is very broad and vague. Please be more specific in explaining what you mean by this term.

This has been corrected according the reviewer's comments.

Line 64: replace “also” with “including”

This has been corrected according the reviewer's comments.

Line 67: Although the claim in this sentence may be true, please provide a justification (e.g., quantify how much is produced worldwide and then cite a reliable reference).

The amount of world pepper production in 2017 is given in the text..

Line 68: The term “severe” is generic. Please be more specific and provide references to support your claims.

The word “severe” was changed to "harsh", more appropriate to describe the climate.

Lines 83-84: Describing the plants as the “object” of the study is unusual. You can simply state that “The sweet pepper (species name) hybrid ‘Roberta F1’, a Polish cultivar important for commercial production, was used in this study.

This has been corrected according the reviewer's comments.

Line 88: When listing a plant type, you need to include the species name as well, not just the common name.

No changes, because peat is not the name of the plant but the substrate with which the mycelium was mixed.

Line 91: What was the timing (e.g., time points or developmental stages) when Bio-Algeen was applied?

The time of the treatment application has been write in the text.

Line 125: please explain what you mean by dilution ranges and how they were prepared

In general, in the description of this method does not give a very detailed information ex. how the dilutions were made. For the reviewer : 10 g of the soil was added to an Erlenmayer flask with 90 ml sterile water and mixed. This is how a 10^-1 dilution of the soil was made. Others dilutions were prepared by introducing 1 ml of the soil solution into 9 ml of distilled water (dilution 10^-2) and so on to obtain the appropriate dilutions. It is a generally accepted microbiology scheme for making soil dilution. In my opinion, this part of the methodology should not be changed.

 Line 147: Change vortex to vortexed and Line 161-162: Delete “were done”.

This has been corrected according the reviewer's comments.

Line 162-163: What program did you use to prepare the PCA plots?

All basic statistical analyses were performed using the Statistica.pl package (10) (Stat. Soft. Inc., Tulsa, OK, USA). The analysis of PCA was performed to determine the basic relationship between biodiversity indices and rhizospheric soils (this description is in the corrected text: lines 172-173; 175-176).

Line 163-165: This sentence is confusing. Please re-write with greater clarity.

Variance analysis (ANOVA) with significant differences were calculated using Tukey’s post-hoc least significance difference (LSD) test at a significance level of p £ 0.05. Also the principal component analysis (PCA) were performed to determine basic relationship between biodiversity indices and rhizospheric soils (this description is in the corrected text: line 173-176).

Line 165: How did you generate the heatmap?

The heatmap was performed using the Statistica.pl package (10) (Stat. Soft. Inc., Tulsa, OK, USA) for the standardised data obtained from the analysis of Biolog EcoPlates at 96h (of carbon utilization patterns of 31 different substrates located on Biolog EcoPlates incubated for 96 h).

Line 179: Delete “The analysis of the results of the 3-year study showed that…”

This has been corrected according the reviewer's comments.

Table 1: The spacing is not consistent for the letters next to the experimental values that indicate statistical significance. Please fix.

Table 1 has been corrected according the reviewer's comments.

Line 190: Could you please provide a brief summary sentence at the end of this paragraph briefly explaining the significance of the stated results? The same comment holds for all other paragraphs in the results section. Simply stating the results in a descriptive manner does not help the reader understand the biological significance of the finding. Your role as the writer is to provide your interpretation briefly in the results section and in detail later in the discussion. Lines 229-231: This is a perfect example of what each results paragraph, or at least each results section, should include as indicated in the previous comment.

Short comments in the Results section have been added to selected subsections (added text visible in the manuscript)

Figure 1: The caption for the figure should describe the meaning of the colored boxes in the figure. Furthermore, for the results displayed in this figure, shouldn’t there be some statistical analysis performed to evaluate whether the abundance of one fungal species in one treatment is significant compared to another treatment?

The colored boxes represent the number of fungal communities; the greater the number of colonies has been marked in  more intense the color (red), the smaller number of fungal colonies in light color (light green); description under the Figure 1. Statistics for the presented data were performed using the UPGMA algorithm and presented in the form of a dendrogram (tree). In the analysis of fungal communities, ANOVA is not used because the data does not meet the normal distribution. 1 remains unchanged as it is legible.

Figure 2: At 100% zoom, the text on the graph is very difficult to read. It needs to be enlarged and the size of the graphs reduced so all three panels can fit on one page, Figure 3: The same comment as with figure 2 regarding text size, but also decimals (“.”) should be used instead of commas (“,”) on the y-axis labels; Figure 4: The arrangement of this figure is very unprofessional, making it very difficult to interpret. Please improve (e.g., at least make sure the y-axis caption doesn’t cover the numbers!); Figure 6: Please fix the axis labels, which have “,” as a decimal instead of “.”

Figures 2-6 have been corrected as suggested by the reviewer

Line 298: change “confirm” to “confirmed”; Line 300: change “in the case” to “for”

It has been corrected as suggested by the reviewer

Line 339: The manuscript you cite for this sentence uses a phrase that is very understandable: “the biotic component of soil quality.” Instead of saying “biological component of the soil”, use the same phrase as the manuscript your citing. It is much clearer.

It has been corrected as suggested by the reviewer

Author Response File: Author Response.pdf