Different Nutritional Regimes in a Tomato Soilless System Affect the Bacterial Communities with Consequences on the Crop Quality
Round 1
Reviewer 1 Report
Comments and Suggestions for Authors The title of the manuscript is too long and could be more effective. Consider revising it to be more concise while still capturing the essence of the research. The abstract would benefit from including more specific quantitative results. Consider adding key data points or percentages to provide a clearer overview of your findings. Please define all abbreviations the first time they are used in the manuscript. For example, "PCR" should be spelled out the first time it appears in line 22. Once defined, use the abbreviation consistently throughout the text. The citation style in the text does not follow the journal's guidelines. Please revise to the required style. For example, in line 36, "[2] and [3]" should be changed to "[2,3]". Line 64 should define "N" the first time it appears in the text. Make sure that all symbols and abbreviations are properly introduced before use. Line 75: Consider moving or deleting the sentence "we included two different tomato varieties and two different dietary regimes". This information would be more appropriate in the Materials and methods section as it relates to experimental design rather than the introduction. Please report the number of plants per treatment in each replicate. Improve the description of the environmental conditions in the greenhouse. Include details of temperature range, humidity levels and light intensity/duration. There seems to be a discrepancy in the timeline of your study. The Materials and Methods section states that seedlings will be planted in 2021, while the Sampling section states that harvesting and sampling will take place in 2017. Please clarify and correct this inconsistency to ensure the accuracy of your experimental timeline. The paper appears to have been hastily written, with weaknesses in the results section, which lacks coherence and proper presentation of data. NOTE: Consider combining the analysis of variance tables 2, 3 and 4 into a single comprehensive table. The quality of the figures must be improved. Figures 2, 3, and 4 require significant enhancement. The current quality is substandard for publication. The quality of the figures used in Figures 2, 3 and 4 is inadequate, more appropriate figures Significant differences between treatments should be highlighted in the labelled figure. In the figures' column labels, remove the commas between the letters indicating statistical significance. For example, change "a, b" to "ab" The method of presenting the results is not appropriateStyle of writing the references in the text and references section is not uniform
I kindly invite the authors to check the manuscript because there are some errors due to punctuation and lack of consistency in the manuscript (such as space between number and unit). Minor revisions of English are suggested.
Comments on the Quality of English LanguageMinor revisions of English are suggested.
Author Response
please see the attachment.
Reviewer 2 Report
Comments and Suggestions for AuthorsThe manuscript entitled "Impact of different nutritional regimes in tomato soilless production on the bacterial communities of the root-growing substrate and consequences on the crop production quality” by Beneduce et al. shows the use of differential nutrition regimes in soilless tomato cultivation and their relationship with the root microbiota. The methods used here are interesting and varied, however, the results descriptions need to be improved.
General
· The manuscript does not have any hypothesis. Can the authors explain their hypothesis?
· The results need to be rewritten.
· The authors use a lot of data that does not appear in the manuscript, and it can be added as a supplemental table.
Specific details
L36: Delete the come between number references.
L36/37: I suggest that the authors combine paragraphs 1 and 2.
L91: I suggest that the authors move the sentence 97/99 close to the treatment description (L91).
L196: the cluster description is not correct. The first three clusters are T0, T2 NBA SL, and the rest of the samples. According to the author's description, they need to use a 4-cluster description, with T0, T1, T2 (without T2 NBA SL), and T2 NBA SL.
L210: Change ‘irrigation regime’ to ‘nutritional regime’.
Figure 2: I don’t understand Figure 2. Please explain better. Why are the dots connected? SE or SD?
L259: is the reduction of AOB and NFB significant? Why are the authors not showing the ANOVA for Time in this case?
L260/261: the authors can show the NosZ, NirK, and Nir S gene data in the supplemental table now.
L262: the sentence is not clear. Which effect is producing the decrease? Time or supplement nutrition?
L280/283: Show the numbers.
Figure 3; this figure has a different name from the previous Figure 1. Please, use the name in all the work. When two letters appear over the bars, remove the comma as well.
L288: this is not correct. In Conchita, there are no significant differences between N20 (ab) and control (b). You can say that there is an increase in N20 in comparison with the control, but it is not significant.
L300: The NBA did not present any significant change either. Please correct or add that the decrease was not significant.
L304/306: If the authors are talking about proportional change, please add the percentage of change.
L309: Please, add a supplemental table with all the parameters used in the PCA and it does not appear described in the manuscript. For example: dry matter, Fe, and Zn content.
L325/326: I think that this affirmation is not correct. Because, when you observe Figure 1, both controls (Conchita and Sweetelle) were grouped followed by the Conchita N20 in T1 and T0032. So, there is no difference between T1 and T2 in this case. Yes, the NBA impact over Sweetelle was greater in T2 in comparison with T1. In conclusion, T2 is a more developed stage than T1.
L335: What bacteria generally increase? Time, variety, or Nutrition? This sentence is not clear.
L386/387: That is not correct. In the ANOVA test, ab is equal to a or b. There was an increase in Ascorbic acid with N20 supplementation, but it was not significant. Please correct.
Author Response
Please see the attachment.
Author Response File: 
Author Response.pdf
Round 2
Reviewer 1 Report
Comments and Suggestions for Authors
Although the authors have addressed some previous concerns, some important revisions are still needed, I recommend major revision with particular attention to the results section and overall language improvement.
Improve sentence structure and connectivity between paragraphs
The introduction about the importance and purpose of the research should be presented first.
The abstract is a bit long.
The abstract should express the results quantitatively in terms of product performance.
The introduction lacks connectors between sentences. Some sentences are useless in the introduction section, please focus on your main points.
Line 23: Change to "0.38".
Line 36: Replace with "characterized
Line 39: Change "advandates" to "advantages
Line 42: Change "ase" to "as
Line 43: Change "inbalances" to "imbalances
Line 52: Change "suppression" to "suppression
Line 52: Change "enanchement" to "enhancement.
In the introduction, explain the relationship between microbial communities and product quality.
Inconsistent use of point decimal numbers, please check and correct throughout the manuscript.
Move experimental layout diagram from Supplementary Materials to main text (M&M)
Standardize the use of brackets (e.g. line 106: electrical conductivity (EC))
Correct capitalization at the beginning of sentences (line 204)
Standardized figure/table references (e.g. line 299: standardized use of "fig"/"figure")
Review all abbreviations - define at first use and maintain consistency.
standardize presentation of data in tables (replace brackets with ± for standard errors).
Merge Tables 1 and 2 for better data presentation.
The quality of the figures is poor and should be improved.
Substantially revise section 3.2 for clarity and organization.
Remove redundant statistical notations (line 236: delete "ANOVA, P<0.05")
Incomplete results have been presented, it is necessary to present completely the process of changes in traits, for example lines 302-303.
Figures and tables are not numbered correctly for example, line 308.
Provide complete captions with definitions for all abbreviations used in figures and tables, The captions should be corrected, what do the letters above the column and bar mean?Figure 4 is ambiguous, and the names of traits and treatments should be presented in full in the figure or defined in the caption.
Some traits such as meaningful elements have been measured in the mentioned materials and method section and also presented in the biplot figure but not presented in the results section. It is better to move from the supplementary file to the main text of the article.
In the first paragraph of the discussion, it is better to describe the observed differences between cultivars in more detail.
In the discussion about archaea, there is a need to explain more about the possible reasons for their population decline.
Line 347: Change"coultivars" to "cultivars"
Line 378: Change "whit" to "with"
Line 379: Fix "becoming" formatting
Line 395: Add space in "Sweetelle postharvest"
Line 396: Change "he" to "the"
Line 423: Change "nutritient" to "nutrient"
Line 431: Change "alongide" to "alongside"
Line 432: Revise phrase "of the on the"
Paragraphs in the discussion section are long and can be broken down into smaller sections.
The discussion is well explained and verified with previous research, but it needs further improvement with updated references and coherence in the reviewed results.
The manuscript contains many typographical and spelling errors and needs major corrections.
Please ensure that abbreviations are defined the first time they are used in the manuscript and abbreviated the next time they are used.
The symbols used in the manuscript are not consistent.
Authors should carefully review the entire manuscript to ensure correct use of English.
Comments on the Quality of English LanguageMajor revisions of English are suggested.
Author Response
Comments and answers, reviewer 1.
Comment 1: Improve sentence structure and connectivity between paragraphs.
R: Thanks for the advice about the sentences structure. The text has been revised and all the paragraphs were checked to have more connectivity.
Comment 2: The introduction about the importance and purpose of the research should be presented first.
R: Thank you for the comment. We moved the part about the purpose of our research at the beginning of the introduction, as suggested.
Comment 3 The abstract is a bit long.
R: Thank you for the advice, we reduced the abstract from 241 to 220 words, keeping the meaningfulness and adding some quantitative information as suggested in the next reviewer comment.
Comment 4 The abstract should express the results quantitatively in terms of product performance.
R: We have added more quantitative data in the abstract, about the product quality attributes.
Comment 5 The introduction lacks connectors between sentences. Some sentences are useless in the introduction section, please focus on your main points.
R: We have changed many parts in the introduction according to the reviewer comment. We removed redundant or unnecessary points and shortened the parts that lacked consistency.
Comment 6 Line 23: Change to "0.38".
Line 36: Replace with "characterized
Line 39: Change "advandates" to "advantages
Line 42: Change "ase" to "as
Line 43: Change "inbalances" to "imbalances
Line 52: Change "suppression" to "suppression
Line 52: Change "enanchement" to "enhancement.
R: We have corrected all the parts, something went missing in the removal of the track changes, even if it was already corrected before the earlier submission. All the mistyping errors were corrected according to the comments, we apologise again for the inconvenient.
Comment 7. In the introduction, explain the relationship between microbial communities and product quality.
R: We are grateful to the reviewer for that suggestion. We have made major changes in the introduction and increased the part when we explain the possible relationship between microbial communities and product quality, stressing more our hypothesis. As we stated in the introduction (lines 74-76 and 80-81) to our knowledge there is no study evaluating the effect of overall microbial communities and N-cycling on the tomato quality. We have reported some studies that focused on specific endophitic microorganisms (Including Thricoderma) and reported variable effects on the product quality.
Comment 8. Inconsistent use of point decimal numbers, please check and correct throughout the manuscript.
R: All decimal numbers have been corrected
Comment 9. Move experimental layout diagram from Supplementary Materials to main text (M&M)
R: We are grateful for the suggestion. The figure S1 has been moved to the main text and commented in the methods section.
Comment 10. Standardize the use of brackets (e.g. line 106: electrical conductivity (EC))
R: Al the brackets have been checked and corrected
Comment 11. Correct capitalization at the beginning of sentences (line 204)
R: Capital letter has been added
Comment 12. Standardized figure/table references (e.g. line 299: standardized use of "fig"/"figure")
R: All references to table and figures have been standardised, thank you for the comment, all necessary corrections have been made.
Comment 13. Review all abbreviations - define at first use and maintain consistency.
R: All the abbreviations have been reviewed and made consistent with the text.
Comment 14. standardize presentation of data in tables (replace brackets with ± for standard errors).
R: All S.E. were reported with ± symbol.
Comment 15. Merge Tables 1 and 2 for better data presentation.
R: According to the reviewer suggestion we have merged table 1 and 2 in a single table (1) that includes all quantitative data and statistical inferences of significative effects. We are grateful for this comment that improved the clearness of the results description.
Comment 16. The quality of the figures is poor and should be improved.
R: We have changed the figures and included vectorial high resolution in the text file. We increased colours contrast and lettering size to improve them. We are grateful for this request that improved the final quality of the figures and the presentation of the results.
Comment 17. Substantially revise section 3.2 for clarity and organization.
R: We agree with the reviewer about the need to better clarify the results of qPCR experiments. The section 3.2 has been revised and reorganized, also according to the merged table1. All the changes are tracked in the lines 244-297.
Comment 18. Remove redundant statistical notations (line 236: delete "ANOVA, P<0.05")
R: Redundant statistical notations have been removed (lines 237, 259, 267, 270)
Comment 19. Incomplete results have been presented, it is necessary to present completely the process of changes in traits, for example lines 302-303.
R: We have implemented the results presentation. The paragraphs 3.2 e 3.3 have been reorganised and full presentation of all the results has been done (lines 257-277 and 337-360).
Comment 20. Figures and tables are not numbered correctly for example, line 308.
R: We are grateful for this observation, all figures and tables have been renumbered according to the other comments, and after it they were carefully checked. Figure S1 is now figure 1, the figure 2 is updated to figure 3 and consequently figures 4 (A-E) and 5 were updated in the text and captions.
Comment 22. Provide complete captions with definitions for all abbreviations used in figures and tables, The captions should be corrected, what do the letters above the column and bar mean?
R: Thanks to the reviewer for the comment: we have updated the captions including the abbreviations used. The letters above the column bars represent the significative differences observed among groups. Different letters evidence statistical significance. We reported the explanation in the figure caption.
Comment 23. Figure 4 is ambiguous, and the names of traits and treatments should be presented in full in the figure or defined in the caption.
R: Figure 4 was one of the graphical summaries of the statistically significant qPCR results. Now it has merged with others in a single figure 3, with names of treatments made more evident and added information in the caption.
Comment 24. Some traits such as meaningful elements have been measured in the mentioned materials and method section and also presented in the biplot figure but not presented in the results section. It is better to move from the supplementary file to the main text of the article.
R: We appreciate the reviewer’s suggestion. In our work we manly focused on the microbiology and possible correlation with some quality parameters of the tomato production. The detailed evaluation of the differences among cultivars and chemical composition (macro and micro elements) falls beyond the scope of this paper and will be published separately. In the PCA analysis we included all compositional features and correlated with microbiological diversity, according to PCR-ARISA profiles. Indeed, very few elements contributed to explain the variability in cultivars/treatments, according to our results. We agree that they must be discussed (e.g. dry matter, Fe) and we made amendment in the discussion session accordingly. Since we already moved several data and figures to the main article text, we think that it is still better to leave the table S3 in the supplementary data. Since we suppose that the previous comment about figure 4 could be also about figure 6 (PCA) we changed the figure accordingly.
Comment 25. In the first paragraph of the discussion, it is better to describe the observed differences between cultivars in more detail.
R: Thanks for the comment and suggestion. We have added a paragraph in the discussion that describes the cultivar and their intrinsic differences, followed by the one that describes the observed differences.
Comment 26. In the discussion about archaea, there is a need to explain more about the possible reasons for their population decline.
R: We added a further explanation with relative reference, to explain the archaeal populations decline. It has not been mentioned in the manuscript, but we also made an attempt to detect Ammonia-Oxidising Archaea in our study, but no PCR product was detected in none of the samples tested. This also testify that soilless systems are often selective a general lower diversity in which bacteria and fungi are favoured while Archaea are not, since soil (as we stated in the discussion, lines 399-401) seems to play a pivotal role in maintaining archaeal diversity and abundance.
Comment 27.
Line 347: Change"coultivars" to "cultivars"
Line 378: Change "whit" to "with"
Line 379: Fix "becoming" formatting
Line 395: Add space in "Sweetelle postharvest"
Line 396: Change "he" to "the"
Line 423: Change "nutritient" to "nutrient"
Line 431: Change "alongide" to "alongside"
Line 432: Revise phrase "of the on the"
R: Thanks for reporting the mistyping errors, all of them have been corrected.
Comment 28. Paragraphs in the discussion section are long and can be broken down into smaller sections.
R: The discussion has been divided into separate sections, according to the results discussed.
Comment 29. The discussion is well explained and verified with previous research, but it needs further improvement with updated references and coherence in the reviewed results.
R: Thanks to the reviewer for the positive comment. We have made many changes in the article, and updated the references in many parts. The reviewer results comments have been extended in the discussion section.
Comment 30. The manuscript contains many typographical and spelling errors and needs major corrections.
R: All typos and spelling errors were corrected.
Comment 31. Please ensure that abbreviations are defined the first time they are used in the manuscript and abbreviated the next time they are used.
R: We carefully checked the manuscript and reported all the abbreviations definitions.
Comment 32. The symbols used in the manuscript are not consistent.
R: All the symbols were carefully checked and amended. We used micro “µ” for some volumes, “±” for S.E and S.D. reported in the tables.
Comment 33. Authors should carefully review the entire manuscript to ensure correct use of English.
R: We reviewed a second time the manuscript and corrected the use of English.
Reviewer 2 Report
Comments and Suggestions for AuthorsAgriculture-3307199
The article “Long-term organic fertilizers as partial substitutes for chemical fertilizers enhance biotic and abiotic nitrogen immobilization and optimize nitrogen fertilizer fate in paddy soils” by Hou et al. The work is very interesting and very well written
Abstract
The objectives and experiment details are not clear in the abstract.
Introduction
Line 2: Add the citation. Please correct.
Line 4: The first citations are 1 and 3. The same is true for lines 6, 3 and 3. Please correct the citations in all the manuscript.
There are further citations with errors throughout the discussion, but this paper lacks line numbers, making it impossible to identify them. Please correct.
Author Response
Comments and answers to the reviewer 2
Comment 1: The work is very interesting and very well written
R: We are grateful for the comment of the reviewer.
Comment 2: Abstract : The objectives and experiment details are not clear in the abstract.
R: We have modified the abstract including more details about the objectives and experimental details
Comment 3: Introduction Line 2: Add the citation. Please correct.
R: We have added the citation requested
Comment 4: Line 4: The first citations are 1 and 3. The same is true for lines 6, 3 and 3. Please correct the citations in all the manuscript.
R: Al the citations in the manuscript were checked and amended according to the comment, thank you for noticing the inconsistencies.
Comment 5: There are further citations with errors throughout the discussion, but this paper lacks line numbers, making it impossible to identify them. Please correct.
R: Thank you for the comment and the uncorrect numeration of the citations. We went through all the manuscript
