Optimal Irrigation and Fertilization Enhanced Tomato Yield and Water and Nitrogen Productivities by Increasing Rhizosphere Microbial Nitrogen Fixation
, Bo Li 1, Jiaqi Zheng 1, Lizhen Mao 4, Mingyu Zhao 1,5, Zhanyang Xu 1 and Feng Zhang 1Round 1
Reviewer 1 Report
Comments and Suggestions for AuthorsThe manuscript entitled ‘’ Optimal irrigation and fertilization enhanced tomato yield, water and nitrogen productivity through increasing rhizosphere microbial nitrogen fixation’’ investigated the effect of irrigation and nitrogen application level on tomato yield, rhizosphere microbial diversities, water and nitrogen productivity. In the text, there are many repetitive words and phrases (especially two or three and in one sentence), furthermore there are some punctuations and grammatical mistakes, so moderate English editing is required.
The paper started with an abstract that is not impressive. The abstract is very long (especially in the result section). The authors should focus on the most important results. I strongly suggest that rewrite this section and only focus on the highlighted results.
There are two points in the introduction section:
In the first paragraph, the authors mention the greenhouse tomato cultivation, but what are the advantages of greenhouse production rather than open field cultivation? It would be beneficial if you could provide some information on the disadvantages of open-field farming, as tomatoes are a specific crop that are grown in both farms and greenhouses (Paragraph one, lines 39-46), it could highlight the novelty of the current research, So, I would suggest that in two or three sentences explain the advantages and disadvantages of these two cultivation systems. Here is a published work that you can use it to improve this gap. https://doi.org/10.3390/agronomy13030916
In the third paragraph, add the results of previous research about nitrogen application on tomato crop, highlight the gap of knowledge in previous research and finally explain how the current research can fill this gap.
Section 2.1. Experimental site -- > add the soil nitrogen amount, because the main aim on the current research is based on the irrigation and nitrogen application level on tomato parameters like nitrogen productivity and …
Lines 130-134: unclear and long sentence!!! Paraphrase this sentence and divide it to two or three sentences.
Line 154-160: …. harvested on 15 March and 23 July, …. -- > This sentence is incorrect about tomato crops. Because the yield of tomato gradually obtains. How did you manage harvesting in exactly these dates??!!!
Figure 2 is unclear. Very small and low resolution. Also, the legends are unclear. I would suggest that replace them (Fig 2. a- d).
3.2. Tomato yield and water and nitrogen productivity -- > 3.2. Tomato yield, water and nitrogen productivity
Figure 3:
Please check the significance letters of Figure 3 (a-d).
Error bars are related to SD or SE? Add the explanation in the Figure caption.
Figure 5:
Add the abbreviation of Principal coordinates analysis in the Figure caption and use it in the text. -- > Principal coordinates analysis = PCA
In the material and method section, bring the software information that used for the Principal coordinates analysis (PCA)
I would suggest and divide the discussion section into four sub-sections as the results and discuss each section separately.
4.1. Tomato growth and biomass
4.2. Tomato yield and water and nitrogen productivity
4.3. Diversities of microbial communities
4.4. Core microbiota and functions
Add the suggestion for the future research in the end of conclusion section.
Comments on the Quality of English Language
Moderate English editing is required.
Author Response
Dear Reviewers
Thanks for taking your time to handle this manuscript. We really appreciate all your comments and suggestions. Please find the itemized responses in below and the revisions in the resubmitted files.
Reviewer #1:
General comments:
The manuscript entitled “Optimal irrigation and fertilization enhanced tomato yield, water and nitrogen productivity through increasing rhizosphere microbial nitrogen fixation’’ investigated the effect of irrigation and nitrogen application level on tomato yield, rhizosphere microbial diversities, water and nitrogen productivity. In the text, there are many repetitive words and phrases (especially two or three and in one sentence), furthermore there are some punctuations and grammatical mistakes, so moderate English editing is required
Reply: Thank you for your comments and suggestions. As to punctuations and grammatical mistakes, we utilized MDPI's language services for editing our manuscript. Thank you again.
Specific comments:
(1) The paper started with an abstract that is not impressive. The abstract is very long (especially in the result section). The authors should focus on the most important results. I strongly suggest that rewrite this section and only focus on the highlighted results.
Reply: Thank you for your suggestions. We rewrite this section as follows:
Irrigation and nitrogen rates have significant effect on greenhouse tomato yields, as well as water and nitrogen use efficiencies, but little is known regarding how rates effect microbiome interactions and how those changes might impact tomato yields. Irrigation and nitrogen application rates have significant effects on greenhouse tomato yields, as well as water and nitrogen use efficiencies, but little is known regarding how these rates affect plant–microbiome interac-tions and how the associated changes might impact tomato yields. In this greenhouse study conducted over two years, the effects of three irrigation levels (moderate deficit with 65–75% water holding capacity threshold, slight deficit with 75–85%, and sufficient irrigation with 85–95%) and four nitrogen application levels (60, 120, 240, and 360 kg ha-1) on tomato growth, yield, water and nitrogen productivity, and rhizo-sphere microbial diversities and functions were investigated. The results demonstrated that the highest to-mato leaf area, dry biomass, yield, and water and nitrogen productivities were obtained under the treatment with sufficient irrigation. With increasing nitrogen application, the tomato leaf area, dry biomass, yield, and water and nitrogen productivity showed a trend of first increasing and then decreasing. Overall, the treatment (N2W3) with sufficient irrigation and 240 kg ha-1 N was associated with the highest tomato growth, yield, and water and nitrogen productivities. Moreover, optimal irrigation and nitrogen application obviously altered the structures of rhizosphere bacterial and fungal communities, particularly recruiting microbiota conferring benefits to tomato growth and nitrogen fixation—namely, Lysobacter and Bradyrhizobium. Ulti-mately, optimal irrigation and nitrogen application significantly increased the relative abundances of func-tions related to carbon, sulfur, and nitrogen metabolism, especially nitrogen fixation. In summary, optimal irrigation and fertilization enhanced tomato yield, as well as water and nitrogen productivity through in-creasing the nitrogen fixation functions of the rhizosphere microbiome. Our results provide significant im-plications for tomato cultivation in greenhouses, in terms of optimized irrigation and fertilization. Thanks again. Lines:13-39 in marked revised manuscript.
(2) There are two points in the introduction section:
In the first paragraph, the authors mention the greenhouse tomato cultivation, but what are the advantages of greenhouse production rather than open field cultivation? It would be beneficial if you could provide some information on the disadvantages of open-field farming, as tomatoes are a specific crop that are grown in both farms and greenhouses (Paragraph one, lines 39-46), it could highlight the novelty of the current research, So, I would suggest that in two or three sentences explain the advantages and disadvantages of these two cultivation systems. Here is a published work that you can use it to improve this gap. https://doi.org/10.3390/agronomy13030916
Reply: Thank you for your suggestions. We added “Tomatoes are planted both in the greenhouse and open fields. Greenhouse tomatoes offer the advantage of year-round production, with controlled environments leading to higher yields, reduced pest issues, and consistent quality. In contrast, field-grown tomatoes are subject to seasonal and climate limitations, which can affect both yield and quality. Amirahmadi et al. (2023) reported that compared to greenhouse tomato cultivation, open-field tomato cultivation had negative environmental impact on human health, ecosystem quality, and resources [3]” in the revised manuscript. Lines:13-39 in marked revised manuscript.
(3) In the third paragraph, add the results of previous research about nitrogen application on tomato crop, highlight the gap of knowledge in previous research and finally explain how the current research can fill this gap.
Reply: Thank you for your suggestions. We added knowledge gap as “However, it is remains unclear that the microbial mechanisms under impacts of nitrogen application on tomato growth and yield.” Studying the impacts of irrigation and fertilization on microbial community and functions will provide valuable insights in microbial mechanisms under impacts of nitrogen application on tomato growth and yield. We also added this in the revised manuscript. Lines:99-101 in marked revised manuscript.
(4) Section 2.1. Experimental site -- > add the soil nitrogen amount, because the main aim on the current research is based on the irrigation and nitrogen application level on tomato parameters like nitrogen productivity and …
Reply: Thank you for your suggestions. We added “The soil available nitrogen (sum of N-NO3- and N-NH4+) contents were 54.6 mg kg-1, 164.7 mg kg-1, 27.5 mg kg-1, and 66.4 mg kg-1 for 2020-Spring, 2020-Autumn, 2021-Spring, and 2021-Autumn season experiments, respectively.” in the revised manuscript. Lines:147-150 in marked revised manuscript.
(5) Lines 130-134: unclear and long sentence!!! Paraphrase this sentence and divide it to two or three sentences.
Reply: Thank you for your suggestions. We revised it as: To explore the optimal irrigation and nitrogen fertilizer application for greenhouse tomato growth, yield, and water and nitrogen productivity, a two-year (2020-2021), four-season greenhouse experiment was conducted. The study also aimed to investigate the microbial mechanisms that promote tomato growth under these optimal conditions. Lines:153-156 in marked revised manuscript.
(6) Line 154-160: …. harvested on 15 March and 23 July, …. -- > This sentence is incorrect about tomato crops. Because the yield of tomato gradually obtains. How did you manage harvesting in exactly these dates??!!!
Reply: Thank you for your suggestions. In fact, the harvested date was the last day that we harvested tomato, after which we finished the experiment. But you are right, that sentence was incorrect. Therefore, we revised this as: In 2020, Spring season tomatoes was from 15 March to 23 July. In 2020, Autumn season tomatoes was from 11 August to 20 December. In 2021, Spring season tomatoes was from 15 March to 25 July. In 2021, Autumn season tomatoes was from 11 August to 19 December, respectively. Thank you again. Lines:185-193 in marked revised manuscript.
(7) Figure 2 is unclear. Very small and low resolution. Also, the legends are unclear. I would suggest that replace them (Fig 2. a- d).
Reply: Thank you for your suggestions. We replaced it in the revised manuscript. Lines:279-280 in marked revised manuscript.
(8) 3.2. Tomato yield and water and nitrogen productivity -- > 3.2. Tomato yield, water and nitrogen productivity
Reply: Thank you for your suggestions. We revised the title of 3.2 as your suggestions in revised manuscript. Line:285 in marked revised manuscript.
(9) Figure 3: Please check the significance letters of Figure 3 (a-d).
Error bars are related to SD or SE? Add the explanation in the Figure caption.
Reply: Thank you for your suggestions. The error bars are standard error, and we added this in the captions of Figures 3, 4, and 7. Lines:325, 347, and 405 in marked revised manuscript.
(10) Figure 5: Add the abbreviation of Principal coordinates analysis in the Figure caption and use it in the text. -- > Principal coordinates analysis = PCA
In the material and method section, bring the software information that used for the principal coordinates analysis (PCA)
Reply: Thank you for your suggestions. We added that information in the method section and the captions of Figure 5. Lines: 246-247 and 363-364 in marked revised manuscript.
(11) I would suggest and divide the discussion section into four sub-sections as the results and discuss each section separately.
4.1. Tomato growth and biomass
4.2. Tomato yield and water and nitrogen productivity
4.3. Diversities of microbial communities
4.4. Core microbiota and functions
Reply: Thank you for your suggestions. You gave us a very good suggestion. Considering that the discussion section was mainly focus on irrigation and fertilization on tomato growth and its microbial mechanisms, we divided the discussion section into two sub-sections 4.1 Tomato growth, yield and water and nitrogen productivity; 4.2 Core microbiota and functions. Your suggestions make discussion clearer, thank you again. Lines: 407 and 464 in marked revised manuscript.
(12) Add the suggestion for the future research in the end of conclusion section.
Reply: Thank you for your comments and suggestions. We added “The molecular mechanisms involved in the recruitment of nitrogen-fixing microbiota by tomato roots under optimal irrigation and nitrogen application require further research.” in revised manuscript. Lines: 531-533 in marked revised manuscript.
Author Response File: 
Author Response.docx
Reviewer 2 Report
Comments and Suggestions for AuthorsThe work contained in this manuscript provides novel information that could be of use in pushing forward the understanding of the interactions between irrigation, fertility and microbial communities. The science seems sound and additional work in terms of the studies, for purposes of this manuscript, seems unnecessary. However, the presentation of the work should be improved. Inefficiencies in word use and grammatical errors make the work difficult to read.
Some specific suggestions are detailed below:
Consider rephrasing opening sentence of the abstract. The first two sentences could be replaced with a sentence such as the following, ‘Irrigation and nitrogen rates have significant affect on greenhouse tomato yields, as well as water and nitrogen use efficiencies, but little is known regarding how rates effect microbiome interactions and how those changes might impact tomato yields.’
The second two sentences of the abstract could be rephrased to eliminate excessive verbiage and include details regarding the irrigation treatment. The irrigation treatments would allow a reader to better appreciate the work based on the abstract. An example is as follows: ‘In this greenhouse study conducted over two years, the effect of three irrigation levels (moderate deficit with 65-75% water holding capacity threshold, slight deficit with 75-85%, and sufficient irrigation with 85-95%) and four nitrogen application levels (60, 120, 240, 17 360 kg ha-1) on tomato growth, yield, water and nitrogen productivity, and rhizosphere microbial diversities and functions were investigated.’
Other potential alterations in the abstract to aid in readability and improve appreciation of readers for the details of the study. Suggestions include the following alterations: ‘As increasing nitrogen application, the tomato leaf area, dry biomass, yield, and water-nitrogen increased to 240 22 kg ha-1 productivity showed a trend of increased first and then decreased. The treatment with 240 22 kg ha-1 nitrogen application had the best performance in improving tomato growth and water and nitrogen productivities. Therefore, the treatment (N2W3) with sufficient irrigation and 240 kg ha-1 N had the highest tomato growth, yield, and water and nitrogen productivities. Compared with the CK commercial standard treatment (sufficient irrigation with 120 kg ha-1), the optimal irrigation and nitrogen application significantly increased yield and water and nitrogen productivities by 105.4%, 49.9%, 36.8%, respectively. Moreover, optimal irrigation and nitrogen application obviously altered structures of rhizosphere bacterial and fungal communities including increases in by recruiting tomato growth benefit and nitrogen fixation microbiota, i.e., Lysobacter and Bradyrhizobium.’
Line 141 'optimal' replacement by 'local standard'
Line 148 The reference [30] in the bibliography is not by the the authors of this manuscript. Therefore, I suspect that the citation number is incorrect.
Line 149 Figure 1. The graphs show irrigation depth over time rather than over growth stage. 'data' on the x axis should be replaced by 'date'. Another option would be to replace the dates with 'days after planting'.
Line 167 leaf area measurements should be based on leaflet measurements. Tomato foliage is compound so it would be more correct to measure leaflets within the compound leaf. It would be sufficient to list that length and width of each of (the number of leaves evaluated or range of leaves evaluated) leaflets or leaves were measured to calculate leaf area. The formula for the calculation of area is unnecessary but the units that it would be reported in could be useful.
189 Soil samples were taken from six of each of which treatments (N1W3 and N2W3)?
Line 193 State that the 48 samples were taken from the two treatments not all treatments.
Line 250 Figure 3. letters of separation in Fig 3B are such that there was an apparent transformation and the numbers were back-transformed or other statistical methodology was used to result in the separation as listed or there is an error that should be evaluated.
Lines 288-289 Doesn't absence of significance in this case show that a change from Nitrogen at 120 to 240 kg/ha does not have influence on bacterial communities?
Comments on the Quality of English LanguageLine 166 'vegative' should be 'vegetative'
Line 225 consider replacing 'improved' with 'increased'
Line 238 'are' should be 'area'
Line 255 Delete 'the' in '...the higher..."
Line 284 Delete 'further'
Line 287 Replace 'studied in this study' with 'evaluated'
Line 296 consider replacement of 'improved' with 'increased'
Line 305 Replace 'markedly' with 'marked' since an adjective is needed in this position of the sentence rather than an adverb.
Line 338 Delete "Detailly,"
Line 366 'Many studies' are mentioned but the citation is singular
Line 368 'some studies' also implies that there is more than one but only one [11] was provided.
Line 372-375 Please rephrase this sentence to improve clarity.
Line 376 'plot' should be 'pot'?
Line 377 'no' should be 'not'
Author Response
Dear Reviewers
Thanks for taking your time to handle this manuscript. We really appreciate all your comments and suggestions. Please find the itemized responses in below and the revisions in the resubmitted files.
Reviewer #2:
The work contained in this manuscript provides novel information that could be of use in pushing forward the understanding of the interactions between irrigation, fertility and microbial communities. The science seems sound and additional work in terms of the studies, for purposes of this manuscript, seems unnecessary. However, the presentation of the work should be improved. Inefficiencies in word use and grammatical errors make the work difficult to read.
Reply: Thank you for your comments and suggestions. As to punctuations and grammatical mistakes, we utilized MDPI's language services for editing our manuscript. Thank you again.
Some specific suggestions are detailed below:
(1) Consider rephrasing opening sentence of the abstract. The first two sentences could be replaced with a sentence such as the following, ‘Irrigation and nitrogen rates have significant affect on greenhouse tomato yields, as well as water and nitrogen use efficiencies, but little is known regarding how rates effect microbiome interactions and how those changes might impact tomato yields.’
Reply: Thank you for your comments and suggestions. You gave me a very good revision, thank you. We revised the manuscript as you suggestion in revised manuscript. Lines: 13-22 in marked revised manuscript.
(2) The second two sentences of the abstract could be rephrased to eliminate excessive verbiage and include details regarding the irrigation treatment. The irrigation treatments would allow a reader to better appreciate the work based on the abstract. An example is as follows: ‘In this greenhouse study conducted over two years, the effect of three irrigation levels (moderate deficit with 65-75% water holding capacity threshold, slight deficit with 75-85%, and sufficient irrigation with 85-95%) and four nitrogen application levels (60, 120, 240, 17 360 kg ha-1) on tomato growth, yield, water and nitrogen productivity, and rhizosphere microbial diversities and functions were investigated.’
Reply: Thank you for your comments and suggestions. We revised the manuscript as you suggestion in revised manuscript. Lines: 22-39 in marked revised manuscript.
(3) Other potential alterations in the abstract to aid in readability and improve appreciation of readers for the details of the study. Suggestions include the following alterations: ‘As increasing nitrogen application, the tomato leaf area, dry biomass, yield, and water-nitrogen increased to 240 22 kg ha-1 productivity showed a trend of increased first and then decreased. The treatment with 240 22 kg ha-1 nitrogen application had the best performance in improving tomato growth and water and nitrogen productivities. Therefore, the treatment (N2W3) with sufficient irrigation and 240 kg ha-1 N had the highest tomato growth, yield, and water and nitrogen productivities. Compared with the CK commercial standard treatment (sufficient irrigation with 120 kg ha-1), the optimal irrigation and nitrogen application significantly increased yield and water and nitrogen productivities by 105.4%, 49.9%, 36.8%, respectively. Moreover, optimal irrigation and nitrogen application obviously altered structures of rhizosphere bacterial and fungal communities including increases in by recruiting tomato growth benefit and nitrogen fixation microbiota, i.e., Lysobacter and Bradyrhizobium.’
Reply: Thank you for your comments and suggestions. We have revised the manuscript according to your suggestions. We greatly appreciate the detailed revisions you made to the abstract section. Lines: 22-39 in marked revised manuscript.
(4) Line 141 'optimal' replacement by 'local standard'
Reply: Thanks for your suggestions. We replaced 'local optimal' by 'local standard' in revised manuscript. Thank you again. Lines: 168 in marked revised manuscript.
(5) Line 148 The reference [30] in the bibliography is not by the the authors of this manuscript. Therefore, I suspect that the citation number is incorrect
Reply: Thanks for your suggestions. You are right, we checked carefully and corrected them in revised manuscript. Thank your very much.
(6) Line 149 Figure 1. The graphs show irrigation depth over time rather than over growth stage. 'data' on the x axis should be replaced by 'date'. Another option would be to replace the dates with 'days after planting'.
Reply: Thanks for your suggestions. We revised the Figure 1 in the revised manuscript as your suggestion. We showed irrigation depth very irrigation time. Moreover, the x axis is date, thus we did not change to days after planting in revised manuscript. Thank you again. Lines: 179-180 in marked revised manuscript.
(7) Line 167 leaf area measurements should be based on leaflet measurements. Tomato foliage is compound so it would be more correct to measure leaflets within the compound leaf. It would be sufficient to list that length and width of each of (the number of leaves evaluated or range of leaves evaluated) leaflets or leaves were measured to calculate leaf area. The formula for the calculation of area is unnecessary but the units that it would be reported in could be useful.
Reply: Thanks for your suggestions. You gave us a new suggestion to measure leaf area. Thank you. In this study, we measure all the leaves. In revised manuscript. we canceled the formula for the calculation of area. The units we transformed to m2. Lines: 202-203 in marked revised manuscript.
(8) Line 189 Soil samples were taken from six of each of which treatments (N1W3 and N2W3)?
Reply: Thanks for your suggestions. Yes, soil samples were taken from six of each of Lines: 223-224 in marked revised manuscript.
(9) Line 193 State that the 48 samples were taken from the two treatments not all treatments.
Reply: Thanks for your suggestions. We added those in the revised manuscript. Lines: 229-230 in marked revised manuscript.
(10) Line 250 Figure 3. letters of separation in Fig 3B are such that there was an apparent transformation and the numbers were back-transformed or other statistical methodology was used to result in the separation as listed or there is an error that should be evaluated.
Reply: Thanks for your comments. As you suggestion, we checked the values in the Fig. 3B. In fact, the value of ET was calculated by sum of irrigation and changed water in soil profile. Line: 320 in marked revised manuscript.
(11) Lines 288-289 Doesn't absence of significance in this case show that a change from Nitrogen at 120 to 240 kg/ha does not have influence on bacterial communities?
Reply: Thanks for your questions. In fact, we found the treatment with sufficient irrigation and 240 kg/ha N (N2W3) obtained the highest tomato growth and yield, thus, we only explored the differences in microbial community between the CK and N2W3 treatments. The results showed that there were little differences in alpha diversity between the CK and N2W3 treatment. However, it did not suggest that nitrogen at 120 to 240 kg/ha does not have influence on bacterial communities, it only indicated that the N2W3 (nitrogen at 240 kg/ha) treatment did not change alpha diversity of bacterial community. At least, it showed that the N2W3 treatment increased tomato growth and yield through recruiting beneficial microbiota, instead of bacterial alpha diversity. Thank you again. We hope this response adequately addresses your question.
(12) Line 166 'vegative' should be 'vegetative'; (13) Line 225 consider replacing 'improved' with 'increased'; (14) Line 238 'are' should be 'area'; (15) Line 255 Delete 'the' in '...the higher..."; (16) Line 284 Delete 'further'; (17) Line 287 Replace 'studied in this study' with 'evaluated'; (18) Line 296 consider replacement of 'improved' with 'increased'; (19) Line 305 Replace 'markedly' with 'marked' since an adjective is needed in this position of the sentence rather than an adverb.; (20) Line 338 Delete "Detailly,"; (21) Line 366 'Many studies' are mentioned but the citation is singular; (22) Line 368 'some studies' also implies that there is more than one but only one [11] was provided.; (23) Line 372-375 Please rephrase this sentence to improve clarity.; (24) Line 376 'plot' should be 'pot'?; (25) Line 377 'no' should be 'not'
Reply: Thanks for your suggestions. Because those suggestions that you have revised for us, we reply together. Thank you very much for revised those writing and grammar mistakes for us and we revised them in the revised manuscript. We also utilized MDPI's language services for editing our manuscript. Thank you again.
Author Response File: Author Response.docx
