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Thanks for carefully improving the mansucript based on reviewers' comments.
[# PeerJ Staff Note - this decision was reviewed and approved by Robert Winkler, a PeerJ Section Editor covering this Section #]
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1. In line 175,"total phenol" still not be changed into "total phenolic content". Please keep consistency throughout the manuscript.
2. In lines 672-677, I noticed that the same paper appears to have been cited twice in the reference list under different numbers. Please check it.
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Please carefully address each comment made by reviewers. Thanks!
**PeerJ Staff Note:** Please ensure that all review, editorial, and staff comments are addressed in a response letter and that any edits or clarifications mentioned in the letter are also inserted into the revised manuscript where appropriate.
1. In lines 110–111, the words “and” and “on” appear in Italics. Please correct them.
2. In line 129, please remove the comma after “whereas”, or place it before “whereas” to make the sentence grammatically correct.
3. In lines 174 and 176, I suggest using “total phenolic content” instead of “total phenol”. Please correct it throughout the manuscript.
4. In line 227, “Fig. Figure 1” seems to be a typographical error. Please use either “Fig. 1” or “Figure 1” consistently throughout the manuscript.
5. In Figure 1B, the placement of the significance indicators (e.g., “a”, “b”) appears a little far from the error bars. Please adjust their position to be consistent with Figures 1A and 1C.
6. For all bar charts where statistical differences are analyzed, please mention the statistical analysis in the figure caption.
7. Figure 3 has a visible border, whereas Figures 1 and 2 do not. Please ensure consistency in figure formatting across all figures.
8. Figure 2D appears to differ from the others in presentation. Please clarify or revise it for consistency.
9. In line 268, the “S” in “Supplementary Table 1” is capitalized, whereas in line 285, “supplementary” in “supplementary figure 1” is written in lowercase. Please ensure consistent formatting throughout the manuscript.
10. In line 313, “(Figure 5À)” appears to contain an incorrect character (“À”). It should be corrected to “(Figure 5A)” for consistency and proper formatting.
11. In line 499, it seems that Nitrososphaeraceae is underlined in the text. Please verify whether this is an unintentional formatting mark and revise it for consistency.
12. It is recommended to review all figures for minor formatting inconsistencies and to standardize their appearance throughout the manuscript.
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In the manuscript entitled “Microbial allies: shaping growth, physiology, and rhizosphere dynamics of onion (Allium cepa L.)”, the dual effects of microbial biofertilizers on the phenotypic performance and rhizosphere microbiome composition of onion were investigated. While I appreciate the author’s efforts in addressing an important topic, the manuscript can be considered for publication after the identified issues are properly addressed.
Some minor comments are highlighted in the pdf file.
Need to add manufacturer information to some lab instruments
For the conclusion section, it may be an overstatement to claim this as “the first global study,” since the dataset is limited to one region. Consider revising the sentence to: “This research represents a novel integrative approach linking metagenomics and agronomic traits in the onion rhizosphere.”
For the final conclusion section, while the conclusion focuses on positive outcomes, a brief mention of limitations (e.g., environmental variability, need for field validation) or future research directions would make the conclusion more balanced and forward-looking.
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