Identifying Bioactive Compounds in Common Bean (Phaseolus vulgaris L.) Plants under Water Deficit Conditions

Round 1

Reviewer 1 Report

Comments and Suggestions for Authors If we want to know the effects of the degree of deficit
on yield reduction and quality, one DI treatment is not enough.
Also, water potential and gas exchange parameters
should be measured continuously during the duration of the experiment in order
to adequately assess the plant's physiological response to drought stress
(it is not enough to measure at the beginning and end of the treatment). Quality parameters, especially phenolic compounds, which are emphasized,
should be performed biochemically and the results presented in absolute values
​​for a better understanding of DI effects.
Therefore, I suggest that additional analyzes be done.

 

Author Response

-Reviewer 1

R: If we want to know the effects of the degree of deficit on yield reduction and quality, one DI treatment is not enough.

A: In our previous experiment with beans, we worked with more levels of irrigation to know the threshold that bean plants were able to withstand without strong reductions in growth and fruit yield. Therefore, the use of this treatment in the present experiment has been conscious, in order to evaluate changes in the metabolomics of the plant, without observing significant production losses. Nevertheless, in the bibliography, there are many articles on which two levels of irrigation are used, (control and deficit irrigation), to see the physiological or growth response in the plant, and these articles have been published without any problem.

 

R: Also, water potential and gas exchange parameters should be measured continuously during the duration of the experiment in order to adequately assess the plant's physiological response to drought stress (it is not enough to measure at the beginning and end of the treatment).

A: The measurements were taken at 4 DAT and 30 DAT of the experiment. Taking into account that the experiment lasted one month, two measurements are enough for the purpose of the experiment. We have many articles in which our objective was evaluate many physiological and growth parameters of plants throughout the time, thus, measurements were taken continuously over the experiment (Gómez-Bellot et al., 2013; Gómez.Bellot et al., 2015; Álvarez et al., 2019; Gómez-Bellot et al., 2024) but this is not the case.

 

 

R: Quality parameters, especially phenolic compounds, which are emphasized, should be performed biochemically and the results presented in absolute values for a better understanding of DI effects. Therefore, I suggest that additional analyzes be done.

A: The identification of all known and unknown small molecules in an organism, referred to as the metabolome, represents the metabolism discoveries. Our target was not getting the absolute value (quantification) of each individual metabolite. This is just possible with pure standards and a ‘targeted metabolomics’ approach. The lack of pure standards commercially available it is an actual bottleneck. Also, a different equipment, UHPLC-Triple Quadrupole, is needed to do so.

  

 

 

Reviewer 2 Report

Comments and Suggestions for Authors

This study assesses the physiological and biochemical responses of Phaseolus vulgaris L. to deficit irrigation. It evaluates whether such stress may positively influence common beans' quality and bioactive metabolite profiles. The study is of interest in the context of climate change and the resulting scarcity of irrigation water. However, the MS needs to undergo revision in most parts. I have made my comments/edits directly in the MS file (attached), which can be summarized as follows:

1-      Please reconsider the title of the paper

2-      The abstract: needs to be carefully revised and the results should be presented specifically referring to the time of the measurements (4 or 30 days after treatment).

3-      The introduction is generally a good shape with some minor revisions required.

4-      In the materials and methods, more detailed information is needed especially for the data analysis.

5-      In the results section, please carefully check the figures and their captions. Please be consistent when using some expressions and terminologies throughout the MS. For instance, in the materials and methods section, 4 and 30 DAT were mentioned while in the results section, 1st and 4th week were used.

6-      I think the discussion is poorly interconnected and lacks an in-depth and comprehensive interpretation of the results, and thus requires careful revision.

More comments and edits can be found in the attached MS file.

Comments for author File: Comments.pdf

Comments on the Quality of English Language

A moderate English language editing is required especially in the results and discussion sections.

Author Response

R: This study assesses the physiological and biochemical responses of Phaseolus vulgaris L. to deficit irrigation. It evaluates whether such stress may positively influence common beans' quality and bioactive metabolite profiles. The study is of interest in the context of climate change and the resulting scarcity of irrigation water. However, the MS needs to undergo revision in most parts. I have made my comments/edits directly in the MS file (attached), which can be summarized as follows:

• Please reconsider the title of the paper+

A: The title has been changed

• The abstract: needs to be carefully revised and the results should be presented specifically referring to the time of the measurements (4 or 30 days after treatment).

A: The abstract has been revised and corrected with the reviewer’s suggestions

• The introduction is generally a good shape with some minor revisions required.

A: Minor revisions have been taken into account.

• In the materials and methods, more detailed information is needed especially for the data analysis.

A: The information required by the reviewer has been added.

• In the results section, please carefully check the figures and their captions. Please be consistent when using some expressions and terminologies throughout the MS. For instance, in the materials and methods section, 4 and 30 DAT were mentioned while in the results section, 1st and 4th week were used.

A: There was a problem in the figures and bars could not been seen properly. They have been replaced. Legends and captions have been corrected and terminology has been unified. 

• I think the discussion is poorly interconnected and lacks an in-depth and comprehensive interpretation of the results, and thus requires careful revision.

A: Discussion has been improved following the reviewer’s suggestions. We think that now sentences are well connected.

 

More comments and edits can be found in the attached MS file.

A: All the comments have been taken into account. Some sentences and words have been marked by the reviewer but with no comments. Therefore, we do not know exactly what he meant, although we think that we have interpreted them correctly.

A: Other answers to his comments:

- We only used Student’s t-test because this is used to compare the means of two groups, while the ANOVA test is used to compare the means of three or more groups.

- There were 30 plants per treatment, with 3 replications per treatment. Each replication consisted of 10 plants in each tray. It has been added to the Ms.

- We calculated SEM (standard error of mean) taking the standard deviation and divided it by the square root of the sample size.

- Regarding reviewer’ comments (line 325) about “What kind of data?”:

We are referring to the fact that there is no available information/data on “untargeted metabolomics” in DI beans.

Regarding reviewer’ comments (326-327) “Is it a must to find previous study to discuss your results?”: The answer is Yes. As we have focus on “novel biomarkers” discovery (untargeted metabolomics) it is a must for us to find any previous study about our “novel metabolites” to be 100% sure that they have not been previously described.

Reviewer 3 Report

Comments and Suggestions for Authors

This study is intriguing and valuable as a reference. However, if the biologically active compounds were quantified, it would enhance the value of the research. I have a few suggestions as follows:

 

In section 2.1. Plant Material and Experiment Conditions, it is necessary to include details on how the experiment was designed and how the treatments were replicated.

 

Figures 1, 2, and 3 need to be adjusted appropriately, specifically noting that the labels for control and DI are not found in the figures.

 

Section 3.3 related to data analysis should be moved to section 2.4 Data treatment in the manuscript. Section 2.4 "Data treatment" should be renamed to "Statistical analyses".

 

Although there are few studies related to the findings of this research, the authors should provide additional suggestions or directions for future research.

Author Response

R: This study is intriguing and valuable as a reference. However, if the biologically active compounds were quantified, it would enhance the value of the research. I have a few suggestions as follows: A: As we commented to Reviewer 1, our goal was not the ‘targeted metabolomics’ approach. The quantification of each significantly different metabolite might be done only under certain circumstances above mentioned.

 

 

R: In section 2.1. Plant Material and Experiment Conditions, it is necessary to include details on how the experiment was designed and how the treatments were replicated.

A: More details have been taking into account.

 

R: Figures 1, 2, and 3 need to be adjusted appropriately, specifically noting that the labels for control and DI are not found in the figures.

A: There was a problem in the figures and bars could not been seen properly. They have been replaced.

 

R: Section 3.3 related to data analysis should be moved to section 2.4 Data treatment in the manuscript. Section 2.4 "Data treatment" should be renamed to "Statistical analyses".

A: As the reviewer suggests, section 3.3 has been placed to section 2.4 and section 2.4 has been renamed.

 

R: Although there are few studies related to the findings of this research, the authors should provide additional suggestions or directions for future research.

A: It has been added.

 

Round 2

Reviewer 1 Report

Comments and Suggestions for Authors

In the future research, when you examine the dynamics of a process, include more points so that the conclusions are more reliable.

Author Response

In the future research, when you examine the dynamics of a process, include more points so that the conclusions are more reliable. Thanks. Suggestions will be taken into account for future studies.

 

Reviewer 2 Report

Comments and Suggestions for Authors

Dear Authors,

Thank you for your efforts in improving the quality of your MS. I believe it is now in a much better shape; however, some points require your attention:

1- The title: You might need to add the "common bean", and the scientific name.

2- The abstract: Please see my suggestions in the MS file (attached).

3- The introduction: some minor edits are required. Please see the attached file.

4- The Materials and Methods: Also some minor edits are needed.

5- The results: The same problem still exists with figures 1-3. So, I cannot say anything about these figures.

6- The Discussion: It is now in a better shape. However, I believe more can be done for further improvement.

7- Some words/sentences are highlighted, meaning that they need your attention.

Comments for author File: Comments.pdf

Comments on the Quality of English Language

Minor English language editing might be required.

Author Response

Thank you for your efforts in improving the quality of your MS. I believe it is now in a much better shape; however, some points require your attention:

• The title: You might need to add the "common bean", and the scientific name.

It has been done.

• The abstract: Please see my suggestions in the MS file (attached).

Suggestions have been taken into account.

• The introduction: some minor edits are required. Please see the attached file.

All suggestions have been taken into account.

• The Materials and Methods: Also some minor edits are needed.

They have been addressed.

• The results: The same problem still exists with figures 1-3. So, I cannot say anything about these figures.

We use sigmaplot program for figures edition. We do not know why the figures cannot been seen. Now, figures have been placed as screenshots. Although the visual quality may have decreased, we hope the problem has been solved.

• The Discussion: It is now in a better shape. However, I believe more can be done for further improvement.

This section has been revised again.

• Some words/sentences are highlighted, meaning that they need your attention.

Most of the highlighted parts have been revised and corrected.

Author Response File: Author Response.pdf