Effective Amendments on Cadmium, Arsenic, Chromium and Lead Contaminated Paddy Soil for Rice Safety
Round 1
Reviewer 1 Report
I reviewed all my comments again and I have to thank to authors for their acceptance and additional explanation.
Author Response
Dear reviewer
I hope this finds you in good health.
Thanks a lot for reviewing my manuscript. I have gone through all of your comments, which were valid, accurate, and to the point. Furthermore, you pointed out the empty loops in my manuscript which I have now fulfilled. I hope my answers are as valid as you will be expecting from me.
Thanks
Response. Minor changes were made in abstract, introduction and result section. The grammatical and spelling mistakes were also addressed in the above sections
Thanks
Reviewer 2 Report
The study examines how different amendments influence the bioavailability of toxic elements. Overall, the topic is important given the increasing contamination of soils in rice production systems. However, I think there are major issues with the presentation of the results and the writing more broadly. I highly suggest the authors find a way to map out the experimental design and be as explicit as possible when detailing the results. I found it very hard to follow the results section as it is currently structured. The section headers should are not easy to interpret. For example, I discourage the use of the treatment IDs (e.g., T7X1 or T9X1) in the section headers.
I understand the challenge in presenting data given the various treatments, but I think it would be helpful to the reader if the authors could find a way to summarize the findings in a cohesive narrative. However, I think after significant revision, this manuscript will be valuable to the readers of Agronomy.
Line 17: Please change the wording in "materials containing thiol group." Do the authors mean materials containing a thiol group?
Line 24-25: The “level two” nomenclature is not clear.
Line 33: I suggest changing “It is potential” to “there is potential.”
Line 34: There is an s in “MHs,” but not in “modified - hair.”
Line 41: Please remove “the” where it states “…contaminated by the uncontrolled industrialization…”
Line 42: Remove “Usually.”
Line 43-44: I would word the end of the sentence as “heavy metal and metalloid contamination.”
Line 45: This is the first instance that the TE acronym is used. Please indicate in parentheses where it is first introduced.
Line 46: The end of this sentence, starting at “process finally reached…” is not clear as written.
Line 49: I suggest replacing “TEs contaminated” to “TE-contaminated.”
Line 50: Remove “These” in the sentence about organic material alone and in combination…
Line 52: I would use “lime” instead of “liming” in this case.
Line 57: Please replace “has capability” with “has the capacity to form…”
Line 79: Please see my comment about the use of “materials containing thiol group.” It is not clear as written.
Last few sentences of the abstract: the authors start using a future tense (will be) that I think is appropriate for a proposal, but not a research article. I would switch the tense here to past tense.
Lines 105-110: I think this information would be better-suited to a table.
Line 135: Do the authors mean salons?
Line 202-204: The description of the PCA results is not entirely clear as written. The axes explain a percentage of the variability, correct? What do the authors mean by “all the elements are diverse”?
Author Response
Dear reviewer
I hope this finds you in good health.
Thanks a lot for reviewing my manuscript. I have gone through all of your comments, which were valid, accurate, and to the point. Furthermore, you pointed out the empty loops in my manuscript which I have now fulfilled. I hope my answers are as valid as you will be expecting from me.
Thanks
The study examines how different amendments influence the bioavailability of toxic elements. Overall, the topic is important given the increasing contamination of soils in rice production systems. However, I think there are major issues with the presentation of the results and the writing more broadly. I highly suggest the authors find a way to map out the experimental design and be as explicit as possible when detailing the results. I found it very hard to follow the results section as it is currently structured. The section headers should are not easy to interpret. For example, I discourage the use of the treatment IDs (e.g., T7X1 or T9X1) in the section headers.
I understand the challenge in presenting data given the various treatments, but I think it would be helpful to the reader if the authors could find a way to summarize the findings in a cohesive narrative. However, I think after significant revision, this manuscript will be valuable to the readers of Agronomy.
All possible changes were made in result section
Point 1: Line 17: Please change the wording in "materials containing thiol group." Do the authors mean materials containing a thiol group?
Response1: Changes were made in line 17.
Point 2:Line 24-25: The “level two” nomenclature is not clear.
Response 2. In line 20 and 21 this matter was addressed.
Point 3 :Line 33: I suggest changing “It is potential” to “there is potential.”
Response 3: it was changed to there.
Point 4:Line 34: There is an s in “MHs,” but not in “modified - hair.”
Response 4: S was added to hairs
Point 5: Line 41: Please remove “the” where it states “…contaminated by the uncontrolled industrialization…”
Response 5: “the” was removed
Point 6:Line 42: Remove “Usually.”
Response 6. “Usually” was removed
Line 43-44: I would word the end of the sentence as “heavy metal and metalloid contamination.”
Response. The “S” was removed
Line 45: This is the first instance that the TE acronym is used. Please indicate in parentheses where it is first introduced.
In line 45 the matter was resolved.
Line 46: The end of this sentence, starting at “process finally reached…” is not clear as written.
Response :”The TEs released through different natural and anthropogenic process finally reached to the soil” it mean all the TEs elements that are released to our environment release through natural or men made process finally reaches our soil as it’s a dumping point of all materials
Line 49: I suggest replacing “TEs contaminated” to “TE-contaminated.”
Response. The changes were made according to your instructions
Line 50: Remove “These” in the sentence about organic material alone and in combination…
Response. The changes were made according to your instructions
Line 52: I would use “lime” instead of “liming” in this case.
Response. The changes were made according to your instructions
Line 57: Please replace “has capability” with “has the capacity to form…”
Response. The changes were made according to your instructions
Line 79: Please see my comment about the use of “materials containing thiol group.” It is not clear as written.
Response. Changed were made in line 80.
Last few sentences of the abstract: the authors start using a future tense (will be) that I think is appropriate for a proposal, but not a research article. I would switch the tense here to past tense.
Response: the changes were made in last few sentences of introduction. I think you were asking about the last sentence of introduction not abstract.
Lines 105-110: I think this information would be better-suited to a table.
Response: I made the table but that didn’t look very nice and occupied a lot of space with poor look than text.
Line 135: Do the authors mean salons?
Response: yes
Line 202-204: The description of the PCA results is not entirely clear as written. The axes explain a percentage of the variability, correct? What do the authors mean by “all the elements are diverse”?
Response: The Principal Component Analysis (PCA) showed a clear difference between various treatment effect on and Heavy metal in rice plant. PCA1 AND PCA2 axis show correlation among treatments. PCA1 is the direction of most variation in total heavy metal concentration in rice plant while PCA2 is the second most variation. So, here PC1 and PC2 represent percentage of variability
The axis’s of (PCA1 and PCA2) I talked about overall variation and that’s why I combines (PCA1= 75.3%) and (PCA2=16.4) and it shows percentage of variability which is 97.1 %, in this PCA1 represent largest percentage of variability and show more variation. PCA 2 is the second axes explaining second more variability.
All the element is diverse mean all the elements show variation and they are different/ varied and have variation among them like
Round 2
Reviewer 2 Report
I unfortunately did not see any major improvement in the manuscript's structure or clarity. I still find the results and discussion very hard to follow and it is challenging to provide concrete suggestions at this stage. As a specific example, in my previous revision, I addressed my concerns with the explanation of the principal component analysis. My original comment was "The description of the PCA results is not entirely clear as written. The axes explain a percentage of the variability, correct? What do the authors mean by “all the elements are diverse”?" The authors did not make any effort to improve the wording in text in response to this comment.
The discussion requires significant reworking. As written it is very hard to follow. For example the paragraph at lines 370-407 is far too long and covers too many different topics. The discussion in general should be pared down and refocused without any specific reference to treatment IDs such as T7X2. Please discuss the treatment effects more broadly in this section.
At lines 435-438 there is reference to the results from a correlation analysis but without any specific interpretation or discussion.
The authors should spend more time with their interpretation and identify ways to distill the findings down to key take-home points.
At this point, I suggest the authors spend significantly more time improving the manuscript as I cannot provide in-depth comments to the manuscript in its current form.
Author Response
Dear reviewer
I hope this finds you in good health.
Thanks a lot for reviewing once again my manuscript and spend your valuable time. I have gone through all of your comments, which were valid, accurate, and to the point. Furthermore, you pointed out the empty loops in my manuscript which I have now fulfilled. I hope my answers are as valid as you will be expecting from me. This time I hope you will find my manuscript improve from previous. I did changes in my manuscript and interpret the PCA analysis, keeping in mind your comments.
Poin1 1: I unfortunately did not see any major improvement in the manuscript's structure or clarity. I still find the results and discussion very hard to follow and it is challenging to provide concrete suggestions at this stage. As a specific example, in my previous revision, I addressed my concerns with the explanation of the principal component analysis. My original comment was "The description of the PCA results is not entirely clear as written. The axes explain a percentage of the variability, correct? What do the authors mean by “all the elements are diverse”?" The authors did not make any effort to improve the wording in text in response to this comment.
Response1 :Thanks for your valuable comment about PCA result. I add supplementary data at the end of the manuscript and interpret the results. Please find the changes and interpretation of PCA results in the following lines. Please go to the lines 201-209, 224-230 and 233-239. I hope it will be clearer and interpretation of the results are improved from previous. I did efforts to improve the wording in text in response to your valuable comments. Your comments are best and I did changes in the above mention lines and did interpretation. I also explained and interpret the axes explanation of variability in more accurate form. If there is need for any improvement let us inform we will incorporate more and will improve it. New supplementary file is also added regarding PCA
Point 2: The discussion requires significant reworking. As written it is very hard to follow. For example the paragraph at lines 370-407 is far too long and covers too many different topics. The discussion in general should be pared down and refocused without any specific reference to treatment IDs such as T7X2. Please discuss the treatment effects more broadly in this section.
Response 2: dear reviewer thanks for pointing out errors in this portion of my manuscript. Changes were made in discussion section. The discussion was further interpreted to increase the understanding of the viewers.
Point 3: At lines 435-438 there is reference to the results from a correlation analysis but without any specific interpretation or discussion.
Response 3: thanks a lot for pointing this section. More information was added to this section in lines 472-477.
Again I am very thankful to the respectable reviewer for his time and valuable comments
Round 3
Reviewer 2 Report
The authors generally addressed all of my previous comments. There are still several areas where the wording or paragraph structure could be improved. Overall, it is much easier to follow.
Line 20-21: I think the description of the two treatment levels (“X2 double of X1”) is somewhat confusing. It may just be a matter of the wording, for example, by saying a low or high, single or double rate. How or why were these particular rates chosen? I would use slightly more descriptive language to guide the reader, because X1 and X2 does not provide relevant information.
Line 44-45: I may have missed this in the last review, but please avoid using “contamination” twice in this sentence.
Line 201: PCA interprets data more meaningfully than what?
Lines 202-220: I appreciate the effort to provide more background for the PCA, but I think there is now too much information and is somewhat difficult to follow. I think some wordsmithing will improve the clarity. For example, the sentence starting with “This basically creates” could be worded as follows: “The analysis creates a new set of axes, rotated in such a way to align maximally with variance, thus distilling high-dimensional data into a few linear combinations.” Please spell out the PCA acronym at the first mention of PCA (first sentence in this section?). The sentence starting with “These clustering techniques” seems a bit redundant since you already describe the analysis at the start of the section.
Line 388: There’s no mention of “HM” until the discussion so I would spell out the acronym here (“heavy metals”).
Line 405-406: I would be more specific when you say a certain treatment was “most significant” – in terms of what?
Line 401-440: This paragraph still feels too long. Is it possible to break this up into two shorter paragraphs?
Author Response
Dear reviewer
I hope this finds you in good health.
Thanks a lot for reviewing my manuscript. I have gone through all of your comments, which were valid, accurate, and to the point. Furthermore, you pointed out the empty loops in my manuscript which I have now fulfilled. I hope my answers are as valid as you will be expecting from me.
Thanks
Point 1: Line 20-21: I think the description of the two treatment levels (“X2 double of X1”) is somewhat confusing. It may just be a matter of the wording, for example, by saying a low or high, single or double rate. How or why were these particular rates chosen? I would use slightly more descriptive language to guide the reader, because X1 and X2 do not provide relevant information.
Response 1: Thanks a lot for pointing out this confusion and providing replacement words. I have replaced X1 and X2 with single and double and made it more readable and understandable.
Point 2: Line 44-45: I may have missed this in the last review, but please avoid using “contamination” twice in this sentence.
Response 2: the word contamination was removed. I am sorry I do not know why I did now noticed it before. Thanks for pointing it out
Point 3: Line 201: PCA interprets data more meaningfully than what?
Response 3: PCA is much better than other traditionally used tools used for analyzing and presenting the data. A short and brief wording was added to paper.
Point 4: Lines 202-220: I appreciate the effort to provide more background for the PCA, but I think there is now too much information and is somewhat difficult to follow. I think some wordsmithing will improve clarity. For example, the sentence starting with “This basically creates” could be worded as follows: “The analysis creates a new set of axes, rotated in such a way to align maximally with variance, thus distilling high-dimensional data into a few linear combinations.” Please spell out the PCA acronym at the first mention of PCA (first sentence in this section?). The sentence starting with “These clustering techniques” seems a bit redundant since you already describe the analysis at the start of the section.
Response 4: The changes are valuable and thanks once again for such a nice suggestion. I am really glad to you; these changes improve my manuscript. I did it according to the reviewer suggestions. Please find the changes in the line mention in the manuscript as follow:
- In the line 204-205 the following changes are made according to your valuable suggestion, it is best and good word addition to my manuscript. “The analysis creates a new set of axes, rotated in such a way to align maximally with variance, thus distilling high-dimensional data into a few linear combinations.
- . Please go to line 200 the spell out the of PCA acronyms at the first sentence of Principal component analysis and interpretation (PCA) is done.
- Please go to line 208-209 line the redundant sentence on the line are deleted. This is repetition and already explained in the start. Thanks for mentioning these changes.
Point 5Line 388: There’s no mention of “HM” until the discussion so I would spell out the acronym here (“heavy metals”).
Response 5: correction was made in this section and “heavy metals (HMs)” was added in the sentence.
Point 6 Line 405-406: I would be more specific when you say a certain treatment was “most significant” – in terms of what?
Response 6: the sentence was restructured and now it provides more information. Highly significant was added and plant and soil information was written in the right place in the sentence
Point 7: Line 401-440: This paragraph still feels too long. Is it possible to break this up into two shorter paragraphs?
Response 7. This paragraph is now much shorter and brief according to your suggestions and was divided into two portions.
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
The article has been improved, but there are some points that need to be addressed:
Clarify response 6. I do not understand what you try to say
Response 7. I tried to say that Cd is less toxic for plants that for animals…see the table 3 (see attached document)(Chaney, R. L.: 1989, ‘Toxic Element Accumulation in Soils and Crops: Protecting Soil Fertility and Agricultural Food-Chains’, in B. Bar-Yosef, N. J. Barrow and J. Goldshmid (eds), Inorganic Contaminants in the Vadose Zone, Springer-Verlag, Berlin, pp. 140–158.
In the abstract, you have to clarify which effect of the amendment cause the change X1 or X2. You have removed this information
You have left most of the mean values ± SE on the text. At least remove the SE, you are repeating a lot of information, this is in the text and tables….
Comments for author File: 
Comments.pdf
Author Response
Dear reviewer
I hope this finds you in good health.
Thanks a lot for reviewing my manuscript. I have gone through all of your comments, which were valid, accurate, and to the point. Furthermore, you pointed out the empty loops in my manuscript which I have now fulfilled. I hope my answers are as valid as you will be expecting from me.
Thanks
Point 1:Clarify response 6. I do not understand what you try to say
Response 1. In response 6 of previous session I wanted to say that when complexation of HMs will increase the availability will decrease. So more HMs were complexed into the soil due to application of our amendments.
Point 2:Response 7. I tried to say that Cd is less toxic for plants that for animals…see the table 3 (see attached document)(Chaney, R. L.: 1989, ‘Toxic Element Accumulation in Soils and Crops: Protecting Soil Fertility and Agricultural Food-Chains’, in B. Bar-Yosef, N. J. Barrow and J. Goldshmid (eds), Inorganic Contaminants in the Vadose Zone, Springer-Verlag, Berlin, pp. 140–158.
Response 2: the point from your side was “Cd is not a phytotoxic element, it is very toxic for animals but not for plants” so I made my statement that Cd is phytotoxic element. Yes I agree that it is more toxic for animals but still scientist terms it phytotoxic and I provide that reference that it’s called phytotoxic in many manuscripts. Again I accept that its more toxic for animals than plants
Point 3:In the abstract, you have to clarify which effect of the amendment cause the change X1 or X2. You have removed this information
Response3 : those lines are added to abstract
Point 4: You have left most of the mean values ± SE on the text. At least remove the SE, you are repeating a lot of information, this is in the text and tables….
Response 4: the SE values will be removed from text and will remain in tables to reduce repetitions
Thanks again for your valuable comments and suggestions
Reviewer 2 Report
I appreciate scientific merit of submitted paper. I have only several additional remarks:
it would be useful to explain what soil was used for pot experiment from Liuyang city? (arable land or grassland or other ones? extractable P,K - you have probably in the mind available P,K? What extractant has been used? page 3 - the basic analysis are from surface horizon? It would be prosperous to have HMs analysis from all soil profile which was used for pot experiment from; page 4 (line 1) is wrote: "Human hairs were collected from different saloons...." Can you explain it in more details? In addition, it would be also interesting to evaluate Cu, Zn and Ni. Why these HMs were not measured?
Author Response
Dear reviewer
I hope this finds you in good health.
Thanks a lot for reviewing my manuscript. I have gone through all of your comments, which were valid, accurate, and to the point. Furthermore, you pointed out the empty loops in my manuscript which I have now fulfilled. I hope my answers are as valid as you will be expecting from me.
Thanks
Point 1: it would be useful to explain what soil was used for pot experiment from Liuyang city? (arable land or grassland or other ones?
Response 1: changes were made in line 90. The soil was collected from rice paddy field and that was arable land.
Point 2:extractable P,K - you have probably in the mind available P,K? What extractant has been used? page 3 - the basic analysis are from surface horizon?
Response 2. The extractible P and K were analysed in soil before treatments application and after harvest they were not calculated as we were focusing on HMs. Beside this our treatments didn’t contain much of above elements so we didn’t focused on it. Information have been added in page 3.
Point 3. It would be prosperous to have HMs analysis from all soil profile which was used for pot experiment from; page 4 (line 1) is wrote: "Human hairs were collected from different saloons...." Can you explain it in more details?
Response 3. The HMs analysis is done from all soil profile in the experiment and additional information about the hairs was added in line 135-136
Point 4: In addition, it would be also interesting to evaluate Cu, Zn and Ni. Why these HMs were not measured?
Response 4: this study focused on Cd, As, Pb and Cr and treatments were designed accordingly. We also thought to add other HMs but this was a short experiment which is a start to big project. We will include other HMs in coming study according to your suggestions.
Thanks again for your valuable comments and suggestions.
