Effect of straw retention and mineral fertilization on P speciation and P-transformation microorganisms in water extractable colloids of a Vertisol

Bai, Shanshan; Ge, Yifei; Yao, Dongtan; Wang, Yifan; Tan, Jinfang; Zhang, Shuai; Peng, Yutao; Jiang, Xiaoqian

doi:https://doi.org/10.5194/egusphere-2024-983

Preprints

https://doi.org/10.5194/egusphere-2024-983

Preprints

15 May 2024

| 15 May 2024

Effect of straw retention and mineral fertilization on P speciation and P-transformation microorganisms in water extractable colloids of a Vertisol

Shanshan Bai, Yifei Ge, Dongtan Yao, Yifan Wang, Jinfang Tan, Shuai Zhang, Yutao Peng, and Xiaoqian Jiang

Abstract. Water extractable colloids (WECs) serve as crucial micro particulate components in soils, playing a vital role in the cycling and potential bioavailability of soil phosphorus (P). Yet, the underlying information regarding soil P species and P-transformation microorganisms at the microparticle scale under long-term straw retention and mineral fertilization is barely known. Here, a fixed field experiment (~13 years) in a Vertisol was performed to explore the impacts of straw retention and mineral fertilization on inorganic P, organic P and P-transformation microorganisms in bulk soils and WECs by sequential extraction procedure, P K-edge X-ray absorptions near-edge structure (XANES), ³¹P nuclear magnetic resonance (NMR), and metagenomics analysis. In bulk soil, mineral fertilization led to increases in the levels of total P, available P, acid phosphatase (ACP), high-activity inorganic P fractions (Ca₂-P, Ca₈-P, Al-P, and Fe-P) and organic P (orthophosphate monoesters and orthophosphate diesters), but significantly decreased the abundances of P cycling genes including P mineralization, P-starvation response regulation, P-uptake and transport by decreasing soil pH and increasing P in bulk soil. Straw retention had no significant effects on P species and P-transformation microorganisms in bulk soils but brought increases for organic carbon, total P, available P concentrations in WECs. Furthermore, straw retention caused greater change in P cycling genes between WECs and bulk soils compared with the effect of mineral fertilization. The abundances of phoD gene and phoD-harbouring Proteobacteria in WECs increased significantly under straw retention, suggesting that the P mineralizing capacity increased. Thus, straw retention could potentially accelerate the turnover, mobility and availability of P by increasing the nutrient contents and P mineralizing capacity in microscopic colloidal scale.

Received: 01 Apr 2024 – Discussion started: 15 May 2024

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Shanshan Bai, Yifei Ge, Dongtan Yao, Yifan Wang, Jinfang Tan, Shuai Zhang, Yutao Peng, and Xiaoqian Jiang

Status: closed

RC1:
'Comment on egusphere-2024-983', Anonymous Referee #1, 06 Jun 2024

In this study, a fixed-site field trial was carried out from 2008 to 2021 to examine the impacts of straw (wheat and maize) retention and mineral fertilization (N, P, and K fertilizers) on soil inorganic P fractions, organic P species and P-transformation microorganisms in bulk soils and water-extractable colloid fractions. The paper presented a very exhaustive scientific work, The manuscript represents an important original contribution to research on soil phosphorus dynamics. As evaluation techniques, the methodology used and the results of excellent scientific quality. I recommend being accepted for publication after the minor revision. Please see the specific comments.
1) L141–Please report if some residue was left after digestion.
2) L183–the spectra was not shown in Fig. S4 ?
3) Line 193–There is a misunderstanding in the description. Should be MEGAHIT was used to the assemble genome from reads (fastq formats)
4) Line 208–the normality distribution (Shapiro–Wilks test), not tests?
5) Fig.2– the caption needs to be corrected, What is “the A and B” in these figures?
6) Fig.4–What is “the A and B” in these figures?
7) Table 3– modify the notes, there are three treatments in the tables.
8) Table 5–there are three treatments in the tables.
9) Table S2: glpA, glpB, glpC, glpK should be italic.
10）Fig.S6– Solution ³¹P NMR spectra of NaOH–Na₂EDTA extracts of bulk soil (A) and water-extractable colloids (WECs, B), not bulk soil (a) and water-extractable colloids (WECs, b).

Citation: https://doi.org/10.5194/egusphere-2024-983-RC1
- AC1: 'Reply on RC1', Xiaoqian Jiang, 16 Jul 2024
  
  The comment was uploaded in the form of a supplement: https://egusphere.copernicus.org/preprints/2024/egusphere-2024-983/egusphere-2024-983-AC1-supplement.pdf
  
  Citation: https://doi.org/10.5194/egusphere-2024-983-AC1
RC2:
'Comment on egusphere-2024-983', Anonymous Referee #2, 07 Jun 2024

This paper described the influences of straw retention and mineral fertilizer on the different phosphorous (P) forms in bulk soil and water-extractable colloid fractions, including the two P forms and their specific P specifies. The addition of P-related metagenomics analysis provides a comprehensive map of P cycling concerning different land management in the field. The results are very interesting to the current studies of P cycling in soils, with advanced technologies applied, which can help better understand P transformation in different fractions, but the paper could be more precise and would benefit from restructuring. The statistical methods you chose need to be further considered with respect to your observation size. The Result section is well written in general, but it would be better to modify some of the Figures and clarify some of your results. The major weakness of this paper, from my perspective, is the unclarification of your highlights, which means the Discussion section should be heavily revised. The bullet points in the Discussion section should be clearly delivered accordingly, a summarized paragraph is recommended for each subsection. Therefore, the recommendation for this manuscript is a major revision.
Material and methods
Line 102- Once you decided to use the abbreviation of all your six treatments, use them consistently for the rest of the manuscript
Line 131: Are there reasons why you only fractionate the 3 treatments?
Line 132: Why do you use 'moist soil samples' for sedimentation? Do you also measure the soil texture?
Line 137: I think you mean 'The mass proportion of particles...'
Line 140: Which method and in which soil/solution ratio (w/v) do you use for pH measurement? As far as I know, there are big differences between the CaCl2, H2O2, and KCl methods. And which instrument do you use (specify all the instrument information you use for your analysis)?
Line 140: Any pretreatment for SOC and TN measurements? The chemical measurements need to be briefly described (apply to the rest of the method section e.g. Line 145, Line 155-Line 156...)
Line 169: Reconsider two 'considered'...
Line 207: Specify the version of SPSS and R you use and cite the relevant references. For R, list the packages you use and find the relevant citations.
Line 216: SEM and PCA may not be applicable considering the size of your observation. Please at least check the degree of freedom to see if your interpretation, especially SEM results, can be regarded as reliable and stable. Otherwise, there are also similar models for a smaller observation size.
Results
Line 231: (Table 1) I guess
Line 238: See above, either use the abbreviations or use the full name across the manuscript. And could you explain why you only measured the 3 treatments, not all of them? I also see differences from Table 1 between the 6 treatments and a significant increase in IP fractions, at least in W1M1F1, for example. Otherwise, I would think only include the 3 treatments in your results and discussion.
Line 240: I personally would recommend avoiding overusing unclear words such as 'obvious', 'change', 'effect', 'little' etc., And better avoid 'for example' in the result section. You either present them or not.
Line 283: 'This indicated that...' This, for me, looks like a Discussion, not a Result.
Line 289: 'all the tested samples' make it clear, as you only fractionated 3 treatments, then better not use 'all'
Line 290: 'Staw retention'. which treatment do you mean? sole straw retention?
Line 293: 'The control treatment caused significant...' This also happened in the previous description. The control should perform as a reference, which means it is not a treatment but a benchmark you need to compare firstly with other treatments (e.g. mineral fertilizer, sloe straw retention). The comparisons between other treatments (other than control) can be performed afterwards.
Line 299- Check grammer
Line 310- Does this mean that the other fractions are more sensitive to P cycling genes ? Is it just because of the low proportion of WECs?
Fig. 1: This is quite interesting that straw retention does not increase the OM in total , but only changes the partitioning of OM in different fractions. While, the sole mineral fertilizer significantly increases the OM in total. How do you harvest the plants with sole mineral fertilizer treatment? Do you leave the roots or bottom stems in the field? Missing in the Method
Fig. 2: Increase the text size of the plot and modify the note.
Fig. 4: It is confusing. You tried to compare the two fractions, but it is hard to read the information and make the reader easily think you were comparing the six treatments... and lack of description of A and B. I suggest remaking the figure
Fig. 5: See comments above... Again, you should always compare them with the control, though you want to compare between two fractions...
Fig. 6 See comments above... check degree of freedom
Table 3: There are only 3 treatments in the table
Table 5: There are only 3 treatments in the table
Discussion
The subtitles should be informative and clear, with bullet points emphasized. In addition, all the figures and tables described and shown in the Result section need to be used and properly referenced in the Discussion section; otherwise, the results do not need to be in the Result section. Cite only the necessary literature.
Line 326- 'to the enhanced organic matter from crops...' see comments above, how did you harvest the crops with sole mineral fertilizer input?
Line 342: 'Consistent with our findings...' Normally, it should be 'consistent with previous studies, our study finds...'. The discussion section is to interpret your data and deliver your findings/opinions to the audience instead of describing other studies.
Line 344: 'Long-term P...' is this also mineral P fertilizer?
Line 346-353: Where is your own data? Please reference it and demonstrate it.
Line 359: I assume you tried to compare with the control treatment?
Line 365: If you want to discuss this, then you need to describe it first the CN or CP ratio first in the Result section and reference it in the Discussion section accordingly.
Line 368: Conclued from Table 1?
Line 371: 'The slight increase ...' confused
Line 372: Combine your own data
Line 376: 'Had remarkable influences on...' make it clear, the influence is increase or decrease?
Line 378-379: It is better to have a solid summary based on your data and findings. This finding is not new as the OM decomposition will release organic acid. I expect to see more interesting results from your data.
Line 381: 'AP'?
Line 383: 'The influences of...' Make your opinions clear with referenced results; how do you define the stronger effect?
Line 394: 'slight increase' is it significant?
Line 395: 'considerable influence...' How much is the influence? increase or decrease?
Line 399: 'Research conducted...' It seems these are not related to your context.
Line 410: 'clay particles'? <2 micrometers will be enough, in my opinion.
Line 419: Check the logic framework and how you get to this conclusion.
Line 422: Check the logic framework and how you get to this conclusion.

Concluding remark:

This manuscript has an interesting dataset, while the current structure is not applicable for publication. I hope that a thorough revision can improve the manuscript so that it can meet the criteria for publication. Good luck!

Citation: https://doi.org/10.5194/egusphere-2024-983-RC2
- AC2: 'Reply on RC2', Xiaoqian Jiang, 16 Jul 2024
  
  The comment was uploaded in the form of a supplement: https://egusphere.copernicus.org/preprints/2024/egusphere-2024-983/egusphere-2024-983-AC2-supplement.pdf
  
  Citation: https://doi.org/10.5194/egusphere-2024-983-AC2

Status: closed

RC1:
'Comment on egusphere-2024-983', Anonymous Referee #1, 06 Jun 2024

In this study, a fixed-site field trial was carried out from 2008 to 2021 to examine the impacts of straw (wheat and maize) retention and mineral fertilization (N, P, and K fertilizers) on soil inorganic P fractions, organic P species and P-transformation microorganisms in bulk soils and water-extractable colloid fractions. The paper presented a very exhaustive scientific work, The manuscript represents an important original contribution to research on soil phosphorus dynamics. As evaluation techniques, the methodology used and the results of excellent scientific quality. I recommend being accepted for publication after the minor revision. Please see the specific comments.
1) L141–Please report if some residue was left after digestion.
2) L183–the spectra was not shown in Fig. S4 ?
3) Line 193–There is a misunderstanding in the description. Should be MEGAHIT was used to the assemble genome from reads (fastq formats)
4) Line 208–the normality distribution (Shapiro–Wilks test), not tests?
5) Fig.2– the caption needs to be corrected, What is “the A and B” in these figures?
6) Fig.4–What is “the A and B” in these figures?
7) Table 3– modify the notes, there are three treatments in the tables.
8) Table 5–there are three treatments in the tables.
9) Table S2: glpA, glpB, glpC, glpK should be italic.
10）Fig.S6– Solution ³¹P NMR spectra of NaOH–Na₂EDTA extracts of bulk soil (A) and water-extractable colloids (WECs, B), not bulk soil (a) and water-extractable colloids (WECs, b).

Citation: https://doi.org/10.5194/egusphere-2024-983-RC1
- AC1: 'Reply on RC1', Xiaoqian Jiang, 16 Jul 2024
  
  The comment was uploaded in the form of a supplement: https://egusphere.copernicus.org/preprints/2024/egusphere-2024-983/egusphere-2024-983-AC1-supplement.pdf
  
  Citation: https://doi.org/10.5194/egusphere-2024-983-AC1
RC2:
'Comment on egusphere-2024-983', Anonymous Referee #2, 07 Jun 2024

This paper described the influences of straw retention and mineral fertilizer on the different phosphorous (P) forms in bulk soil and water-extractable colloid fractions, including the two P forms and their specific P specifies. The addition of P-related metagenomics analysis provides a comprehensive map of P cycling concerning different land management in the field. The results are very interesting to the current studies of P cycling in soils, with advanced technologies applied, which can help better understand P transformation in different fractions, but the paper could be more precise and would benefit from restructuring. The statistical methods you chose need to be further considered with respect to your observation size. The Result section is well written in general, but it would be better to modify some of the Figures and clarify some of your results. The major weakness of this paper, from my perspective, is the unclarification of your highlights, which means the Discussion section should be heavily revised. The bullet points in the Discussion section should be clearly delivered accordingly, a summarized paragraph is recommended for each subsection. Therefore, the recommendation for this manuscript is a major revision.
Material and methods
Line 102- Once you decided to use the abbreviation of all your six treatments, use them consistently for the rest of the manuscript
Line 131: Are there reasons why you only fractionate the 3 treatments?
Line 132: Why do you use 'moist soil samples' for sedimentation? Do you also measure the soil texture?
Line 137: I think you mean 'The mass proportion of particles...'
Line 140: Which method and in which soil/solution ratio (w/v) do you use for pH measurement? As far as I know, there are big differences between the CaCl2, H2O2, and KCl methods. And which instrument do you use (specify all the instrument information you use for your analysis)?
Line 140: Any pretreatment for SOC and TN measurements? The chemical measurements need to be briefly described (apply to the rest of the method section e.g. Line 145, Line 155-Line 156...)
Line 169: Reconsider two 'considered'...
Line 207: Specify the version of SPSS and R you use and cite the relevant references. For R, list the packages you use and find the relevant citations.
Line 216: SEM and PCA may not be applicable considering the size of your observation. Please at least check the degree of freedom to see if your interpretation, especially SEM results, can be regarded as reliable and stable. Otherwise, there are also similar models for a smaller observation size.
Results
Line 231: (Table 1) I guess
Line 238: See above, either use the abbreviations or use the full name across the manuscript. And could you explain why you only measured the 3 treatments, not all of them? I also see differences from Table 1 between the 6 treatments and a significant increase in IP fractions, at least in W1M1F1, for example. Otherwise, I would think only include the 3 treatments in your results and discussion.
Line 240: I personally would recommend avoiding overusing unclear words such as 'obvious', 'change', 'effect', 'little' etc., And better avoid 'for example' in the result section. You either present them or not.
Line 283: 'This indicated that...' This, for me, looks like a Discussion, not a Result.
Line 289: 'all the tested samples' make it clear, as you only fractionated 3 treatments, then better not use 'all'
Line 290: 'Staw retention'. which treatment do you mean? sole straw retention?
Line 293: 'The control treatment caused significant...' This also happened in the previous description. The control should perform as a reference, which means it is not a treatment but a benchmark you need to compare firstly with other treatments (e.g. mineral fertilizer, sloe straw retention). The comparisons between other treatments (other than control) can be performed afterwards.
Line 299- Check grammer
Line 310- Does this mean that the other fractions are more sensitive to P cycling genes ? Is it just because of the low proportion of WECs?
Fig. 1: This is quite interesting that straw retention does not increase the OM in total , but only changes the partitioning of OM in different fractions. While, the sole mineral fertilizer significantly increases the OM in total. How do you harvest the plants with sole mineral fertilizer treatment? Do you leave the roots or bottom stems in the field? Missing in the Method
Fig. 2: Increase the text size of the plot and modify the note.
Fig. 4: It is confusing. You tried to compare the two fractions, but it is hard to read the information and make the reader easily think you were comparing the six treatments... and lack of description of A and B. I suggest remaking the figure
Fig. 5: See comments above... Again, you should always compare them with the control, though you want to compare between two fractions...
Fig. 6 See comments above... check degree of freedom
Table 3: There are only 3 treatments in the table
Table 5: There are only 3 treatments in the table
Discussion
The subtitles should be informative and clear, with bullet points emphasized. In addition, all the figures and tables described and shown in the Result section need to be used and properly referenced in the Discussion section; otherwise, the results do not need to be in the Result section. Cite only the necessary literature.
Line 326- 'to the enhanced organic matter from crops...' see comments above, how did you harvest the crops with sole mineral fertilizer input?
Line 342: 'Consistent with our findings...' Normally, it should be 'consistent with previous studies, our study finds...'. The discussion section is to interpret your data and deliver your findings/opinions to the audience instead of describing other studies.
Line 344: 'Long-term P...' is this also mineral P fertilizer?
Line 346-353: Where is your own data? Please reference it and demonstrate it.
Line 359: I assume you tried to compare with the control treatment?
Line 365: If you want to discuss this, then you need to describe it first the CN or CP ratio first in the Result section and reference it in the Discussion section accordingly.
Line 368: Conclued from Table 1?
Line 371: 'The slight increase ...' confused
Line 372: Combine your own data
Line 376: 'Had remarkable influences on...' make it clear, the influence is increase or decrease?
Line 378-379: It is better to have a solid summary based on your data and findings. This finding is not new as the OM decomposition will release organic acid. I expect to see more interesting results from your data.
Line 381: 'AP'?
Line 383: 'The influences of...' Make your opinions clear with referenced results; how do you define the stronger effect?
Line 394: 'slight increase' is it significant?
Line 395: 'considerable influence...' How much is the influence? increase or decrease?
Line 399: 'Research conducted...' It seems these are not related to your context.
Line 410: 'clay particles'? <2 micrometers will be enough, in my opinion.
Line 419: Check the logic framework and how you get to this conclusion.
Line 422: Check the logic framework and how you get to this conclusion.

Concluding remark:

This manuscript has an interesting dataset, while the current structure is not applicable for publication. I hope that a thorough revision can improve the manuscript so that it can meet the criteria for publication. Good luck!

Citation: https://doi.org/10.5194/egusphere-2024-983-RC2
- AC2: 'Reply on RC2', Xiaoqian Jiang, 16 Jul 2024
  
  The comment was uploaded in the form of a supplement: https://egusphere.copernicus.org/preprints/2024/egusphere-2024-983/egusphere-2024-983-AC2-supplement.pdf
  
  Citation: https://doi.org/10.5194/egusphere-2024-983-AC2

Shanshan Bai, Yifei Ge, Dongtan Yao, Yifan Wang, Jinfang Tan, Shuai Zhang, Yutao Peng, and Xiaoqian Jiang

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https://doi.org/10.5194/egusphere-2024-983-supplement

Shanshan Bai, Yifei Ge, Dongtan Yao, Yifan Wang, Jinfang Tan, Shuai Zhang, Yutao Peng, and Xiaoqian Jiang

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Short summary

Mineral fertilization led to increases in total P, available P, high-activity inorganic P fractions and organic P, but decreased the abundances of P cycling genes by decreasing soil pH and increasing P in bulk soil. Straw retention brought increases for organic C, total P, available P concentrations in water-extractable colloids (WECs). Abundances of phoD gene and phoD-harbouring Proteobacteria in WECs increased under straw retention, suggesting that the P mineralizing capacity increased.


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