Review Reports

Round 1

Reviewer 1 Report (New Reviewer)

Comments and Suggestions for Authors

1. Title is clear, specific, and scientifically accurate. However:
   1. “semi-hydroponic system” should be used to better reflect the experimental context instead of “greenhouse”.
   2. “Synergistically” should be eliminated because interaction effects should have been statistically significant for most variables, while currently interaction was significant only for soluble solids.
2. Abstract is well structured. However:
   1. The background is inadequate due to the lack of novelty and necessity of the study.
   2. Please mention experimental design and number of replicates.
   3. Please ensure lycopene units match Results section.
   4. In lines 23–24, “PGPR consortia” should be “PGPR consortium”.
   5. “chemical fertilization control” should have formula.
   6. “(80:20)” was based on what unit?
   7. Please clarify whether interactions were significant. Numeric data should be included.
   8. As mentioned above, “Synergistic” effect is not strongly supported across all variables.
3. Keywords should be arranged alphabetically. Moreover, terms appearing in the title should not be included here.
4. Introduction has strong justification for PGPR and vermicompost. However,
   1. The length of the section is inadequate. Please expand it on the current issues, the soilless production, and success in PGPR studies.
   2. “Studies” should be cited with more literatures.
   3. Punctuations should be checked. Moreover, Latinate names should be italicized.
   4. Currently, the introduction lacks a clearly stated hypothesis.
5. Materials and methods are generally well structured. However,
   1. Average temperature and humidity conditions during experiment should be added.
   2. In line 86, “river sand and perlite” should be clarified which river it was.
   3. “chemical fertilization” should be specified with “P” because only P element was used.
   4. Where was the V253 vermicompost description?
   5. Vermicompost EC = 6.6 dS.m^-1. This is relatively high salinity. Please explain.
   6. Please provide strain accession numbers or origin reference and clarify whether compatibility tests were performed.
   7. How was equal proportion in consortium ensured?
   8. Writing mistakes are abundant. Please check.
   9. Statistical analysis must include statistical software and normality and homogeneity testing
6. Results have clear reporting and appropriate interpretation. However:
   1. Figures are overloaded
   2. Please add F-values and p-values to tables for transparency and include sample size in figure captions
   3. You report yield up to 5.2 kg.m^-2 (sixth bunch), but in Methods harvesting was up to eighth bunch. This inconsistency must be corrected.
   4. Please ensure unit consistency.
   5. “No significant interaction detected” is frequently mentioned. Thus, please avoid overuse of “synergistic”. Moreover, the data suggest additive rather than synergistic effects.
   6. Figures 4 and 5 lacks explanation. Moreover, in line 349, it should be “Figure 5”.
7. Discussion has strong mechanistic explanations. However,
   1. It is too lengthy and fragmented without clear subsections. Please add them to divide the discussion.
   2. Some statements were not measured in your experiment. Please avoid bringing external quantitative values unless clearly cited and contextualized. Therefore, claims need references.
8. Conclusions are clear, concise, and acceptable.

Author Response

"Please see the attachment."

Author Response File: Author Response.pdf

Reviewer 2 Report (Previous Reviewer 2)

Comments and Suggestions for Authors

Manuscript ID: Crops-4179899

Title: Vermicompost-based substrates and bacterial consortia synergistically improve the nutraceutical quality of greenhouse tomato (Solanum lycopersicum L.)

 

In this study, the authors evaluated the effects of substrate type and bacterial inoculation on the yield and nutraceutical quality of tomato in a semi-hydroponic system. They concluded that, under the tested conditions, tomato quality is better when plants are grown phosphorus enriched vermicompost and subjected to bacterial inoculation.

The topic is well aligned with the scope of Crops. It is timely and with relevant for tomato production. Overall, the manuscript is logically organized and generally well-written. The language is mostly fluent, although some typographical errors do occur. Thus, it would be necessary to check the language throughout. However, several points need clarification before the manuscript can be considered for publication.

 

Major comments

The general aim of this manuscript is useful for understanding tomato responses to substrate type and bacterial inoculation. However, statistical analysis and interpretation of results are not adequate.

The authors stated in the abstract that they aimed to “evaluate the impact of different growth substrates, combined with plant growth-promoting rhizobacteria (PGPR) inoculation on the yield and nutraceutical quality of tomato”, suggesting that two factors (substrate type and bacterial inoculation) and their interaction are under analysis. However, the statistical analysis alternates between one-way ANOVA (six treatments) and two-way ANOVA (substrate type x inoculation) with no clear emphasis on interaction effects. Therefore, the authors should clarify why they use both statistical approaches and align the analysis with the stated factorial design.

The Abstract is well-written, but would benefit from the inclusion of quantitative values (e.g., percentage increases/decreases or absolute values).

The Introduction is short and not very well structured. It contains four general paragraphs that should to be better contextualized. The introduction should present a coherent background on the topic, clearly define the research gap and explain the novelty of the study. Therefore, the section should be revised for clarity.

The Material and Methods section requires substantial revision to improve clarity, transparency, and reproducibility. Some essential information is missing. In particular:

• A clear justification for selecting the “inert substrate” (is this substrate the “common substrate” for tomato cultivation?
• Physical and chemical properties of each substrate, not only the vermicompost enriched with 442 ppm P (line 91-93).
• The rationale for selecting the bacterial consortium and the amount applied per pot.
• Conditions of the germination period (if it occurred in the same greenhouse)
• Clarification of the transplanting time (35 days after germination or 35 days after sowing).
• Clarification of inoculation at 35 days (in the polystyrene trays or in the polyethylene bags).
• Description of cultivation practices during the experimental period (e.g., tutoring system mentioned in line 385).
• Clarification of the experimental duration (100 DAS?)
• The statement “A completely randomized factorial design with six treatments and three replicates was employed” is incorrectly presented. The design includes three substrate types x two bacterial inoculation, with three replicates, totaling 18 pots.
• The number of growth variables is limited. Plant height measurements should be better described, since only final values are presented. The rationale for using root fresh weight instead of shoot fresh weight should be explained, as well as the option of fresh weight rather than dry weight.
• The statistical analysis should be explained more clearly. It is important to clarify which ANOVA approaches is primary, as this affects the presentation and interpretation of the results. It is unclear if the fruit quality parameters were analysed similarly (line 251). The statistical software used and assumptions (e.g., homogeneity of variance) should be included.

The Results section is repetitive. The inclusion of numerical values (e.g., percentage increases or decreases relative to the control) would improve clarity and interpretability. In this section, all tables and figures need improvement (as indicated in “other comments”).

In the Discussion section, results should be interpreted in relation to the two main studied factors and their interaction. The opening sentence claims that “This study demonstrates that the choice of growth substrate and the application of a PGPR consortium significantly influence the growth, yield, and particularly the nutraceutical quality of greenhouse tomatoes “, but the interactions are non-significant for most of the studied parameters. This fact should be discussed. The section also lacks a clear structure. For example, discussion of health effects (lines 360-366) is followed by plant height and root weight. Some interpretations are not well supported or extend beyond the data. For example, statements attributing fruit size increases to vermicompost require better justification (line 395). Several passages (e.g., lines 426–446) should be reconsidered. Future research should be placed at the end of the section.

The Conclusion, although consistent with the main findings, should be more cautions, as refer to one season and to specific substrate conditions. Therefore, it should be revised.

 

Other comments

The placement of Figure 1 should be revised.

Table 1 describes treatments, not the bacterial consortium as indicated in line 100. Therefore, indication of Table 1 should be revised.

Clarify the sentence in line 109 “These were filled with a substrate composed of vermicompost and river sand (80:20, v/v)”, as it suggests that all pots were filled with the same material.

Crop stages should be defined more precisely. The timing of a) pre-flowering, b) flowering, and c) production should be indicated. The water requirements (0.5, 1 and 2 L per pot?) and frequency should be included

Clarify the definition of “commercial-sized fruits” (line 156). The “average fruit size” (line 154) should appear in the results section.

The placement of reference [18] should be revised, as it refers to the extraction method.

In line 264, Figure 1 is incorrectly indicated.

All figures and tables should be revised for clarity and consistency. In table 1, T6 is incomplete and “pmp” should be corrected to “ppm”. In Figures 2b and 2d, it is incorrect to include a line linking all treatments, since this methodology is more appropriate when time is a variable. The substrate labelled “Chem” should be changed to “CF”, as indicated in Table 1. The header in this figure should explain the meaning of the abbreviations used, as well as the meaning of the circles in each bar. As the bars are different sizes, it is also necessary to explain if the size represents the standard error or the standard deviation. 'Equal numbers in the treatment bars' is incorrect. It should be 'letters'. Table 2 and its header should be revised. Including “plants” at the end of the text is incorrect. The expression 'Mm' should be changed to 'mm' (unit). The labelling of treatments and factors should also be revised. T1 to T6 are not substrate types (TP) and 'fertilization' is not the correct factor. The factors should be presented consistently throughout the document. 'Ns' should be changed to 'ns'. The same applies to Table 3. In Figure 3, 'treatments' should be changed to 'substrate type'. As previously explained, the use of lines to link the different values is incorrect. In line 349, Figure 2 should be Figure 5. The header and the line to link all treatments should be revised in this figure as well as in Figure 4.

Ensure consistency in yield determination (sixth – line 286 vs eighth bunch – line 155).

The sentences in lines 298-301 are more appropriate in the Dscussion. The second sentence should be revised because a significant interaction does not mean a synergetic effect.

The statement in line 316 that 'a significant interaction effect (p < 0.05) was observed for certain metabolites' is incorrect. As indicated in Table 3, there were no significant interactions. Please revise this.

All references should be revised and formatted according to the journal´s guidelines.

Author Response

Please see the attachment.

Author Response File: Author Response.pdf

Reviewer 3 Report (New Reviewer)

Comments and Suggestions for Authors

This manuscript investigates the synergistic effects of vermicompost-based substrates with varying phosphorus levels and PGPR inoculation on the yield and nutraceutical quality of greenhouse tomatoes. The results suggest that vermicompost based substrate, particularly one with a higher phosphorus content, in combination with PGPR inoculation, is a promising strategy to enhance the accumulation of health-promoting bioactive compounds in tomato fruits. The topic is of interest, the experimental design is sound, the methodology is generally robust, and the results are clearly presented with appropriate statistical analyses. Some points should be improved as following.

Line 91: can you provide the physicochemical characteristics of the V253?

Line 92: the pH of the V442 vermicompost is reported as 9.14, which is highly alkaline. The authors should provide an explanation for this high pH. This is critical as high pH can affect nutrient availability and could be a confounding factor in the results. Please discuss this in the manuscript.

Line 249: please check the unit is dry weight or fresh weight (FW in the Table 3).

Line 264: “Figure 1a” is replaced to “Figure 2a”. Please ensure the figure numbering and citing in the text are correctly matched.

Line 282 (Figure 2 caption): The caption says "Equal numbers in the treatment bars indicate non-significant differences". It should likely be "Equal letters" as is standard in other figures.

Table 2: please check the data in the factorial analysis summary at the bottom of Table 2, the yield values for V253 and V442 appear to be swapped based on the treatment data, as it seems V442 treatments (T5/T6) had a higher average yield than V253 treatments (T3/T4), which contradicts the "b" and "c" rankings in the summary. Also check the PD and ED values.

Figure 3: the data was repeated with Table 2, please delete this figure.

Figures 4 and 5: the data were repeated with Table 3. You can select one: keep the figures or delete the data of lycopene and vitamin C in the Table 3.

Line 348: the y-axis label should be vitamin C, and the unit is wrong.

Table 3: The headers are very cluttered. Please simplify. For example, instead of "mg AA 100 g-1 FW", you can use "Vitamin C (mg 100 g⁻¹ FW)". Similarly, for lycopene, use "Lycopene (mg 100 g⁻¹ FW)". This makes the table much easier to read. And the row "ST * BC" has "ns" for all columns. It would be clearer to state in the footnote that "ns" means non-significant (p > 0.05).

Lines 461-462: the conclusion states the findings provide growers with a "clear choice" between maximizing production or nutritional quality. While true, the manuscript would benefit from a more nuanced suggestion. For example, the authors could briefly mention that integrated strategies (like optimizing the vermicompost-PGPR system or exploring reduced chemical fertilizer combined with bio-inoculants) could be a future path to narrow the yield gap while still improving quality, rather than presenting it as a strict binary choice.

References: check for consistent formatting (e.g., some have titles in sentence case, others in title case).

 

Author Response

Please see the attachment.

Author Response File: Author Response.pdf

Round 2

Reviewer 1 Report (New Reviewer)

Comments and Suggestions for Authors

After the first revision, the quality of the manuscript has been improved. However, several issues need revision.

Reduce the methods in abstract

Please make a conclusion meet the objectives; and make it shortly

Author Response

Please see the attachment

Author Response File: Author Response.pdf

Reviewer 2 Report (Previous Reviewer 2)

Comments and Suggestions for Authors

I appreciate the efforst of all authors to improve the manuscript. Overall, the revised version is better than the previous one; however, it still contains several statements that require further revision for clarity, accuracy, and consistency. Please see the attached file for my detailed comments and suggestions. In my opinion, the manuscript still requires major corrections before it can be considered for publication.

 

Comments for author File: Comments.pdf

Author Response

Please see the attachment

Author Response File: Author Response.pdf

This manuscript is a resubmission of an earlier submission. The following is a list of the peer review reports and author responses from that submission.

Round 1

Reviewer 1 Report

Comments and Suggestions for Authors

Overall comments

The manuscript entitled “Vermicompost enriched with phosphorus and bacterial consortia improves the nutraceutical quality of tomato (Solanum lycopersicum L.)” seems to be well-designed, however, the manuscript is poorly written. In my opinion, the MS needs major modifications before accepting for publication to this journal.

 

Major comments

(a) Materials and methods need modifications, particularly the Carotenoids and Flavonoids parts should be concise. No need to use the equation or formula.

(b) Data presentation through tables and figures should be improved and table and figure should be referred to in the text of the results parts.

Specific comments

(a)The figures’ qualities are very poor.  Figure 2 should be improved as the text is unclear. The font size within the figure should be the same. Select suitable color contrast so that they can easily be visible.

(b) Color figures should be made in case of figure number 3, 4 and 5.

(d) Figure number should be corrected and should be referred to text; figure number 2 after figure 4 should be corrected.

(c)Improper citation style throughout the MS. Suppose Line 395, These findings align with those reported by [30,31], should be These findings align with those reported by Barboza-García et al. [30] and Coronel et al. [31].

(d)Plenty of type-setting errors throughout the MS. Authors should revise them accordingly. Suppose Line 264, Glutation should be Glutathione.

Reviewer 2 Report

Comments and Suggestions for Authors

The manuscript Crops-3931324 entitled “Vermicompost enriched with phosphorus and bacterial consortia improves the nutraceutical quality of tomato (Solanum lycopersicum L.)” investigates an important topic for tomato production by combining phosporus enrichment and bacterial inoculation in vermicompost. However, the authors fail to demonstrate this. Despite the novelty of the topic, the experimental design is completely inadequate for analysing the simultaneous effects of phosphorus addition and bacterial consortia, as indicated by the title. To properly analyse the effect of phosphorus in vermicompost and its combination with bacterial inoculation, the edaphic matrix must be identical in all treatments, with phosphorus content being the only factor that varies. In this manuscript, however, the control treatment is a mixture of river sand and perlite (Multiperl®, Mexico) at a ratio of 80:20 (v/v), whereas the other two treatments consist of vermicompost and river sand at a ratio of 80:20 (v/v). The treatments also differ in their physical and chemical composition (pH, electrical conductivity, and nutrient content), which impedes any valid comparison and makes it impossible to attribute the observed differences specifically to phosphorus or bacterial inoculation. Correcting this issue would require a complete redesign and repetition of the experiment, using the same edaphic matrix, and different phosphorus levels. However, if the main focus of the manuscript is changed to the effect of the substrate instead of phosphorus fertilisation, while maintaining bacterial inoculation as a factor, the data could be reanalysed and the results could also be relevant. Alternatively, the effect of bacterial inoculation could be analysed separately within each substrate type. Both approaches exceed a standard revision. For these reasons, I recommend rejecting the manuscript at this time, but encouraging resubmission after a substantial revision.