Spatial and Temporal Variability of the Microbiological and Chemical Properties of Soils under Wheat and Oilseed Rape Cultivation

Round 1

Reviewer 1 Report (New Reviewer)

 

General comment: the manuscript tackles the temporal and spatial variability of the microbiological and chemical properties of soils under wheat and oilseed rape cultivation. This study is interesting; however, methods should be improved. Also, some important results are not properly discussed (spatial trends). Thus, these sections should be improved.

 

Abstract

Line 20. Replace %N by N in the manuscript.

Lines 21-23. Is it possible to assess soil productivity only based on DHA and microbial biomass?

 

Introduction                          

Comments. Some aspects about soil enzyme should be amended. If an important factor was the N content, why did you measure DHA instead of other enzymes related to N cycle? After reading the introduction, it is not clear the reason for assessing the spatial variation of the mentioned soil properties considering the relation with N in gran and seeds.

 

Line 35. Please amend “physio-chemical”, replace it by physicochemical or physico-chemical.

Lines 35-36. Yes, but this occurs in agricultural lands, can you specify it?

Lines 50-51. High variability? Low variability?

Line 80. Please change “Bastiad” by “Bastida”.

Line 105. Why tillage? Can you introduce soil enzymes in a general agricultural context?

Lines 106-107. Soil enzyme activities do not always represent the physiologically active microorganisms, extracellular enzymes might be stabilized on organomineral components of the soil matrix, where they can still show catalytical activity.

Line 108. Which group of enzymes?

Lines 109-110. Please rephrase, you can better introduce DHA (e.g., from soil enzyme activities, DHA…) since the current writing suggests that DHA was previously tackled.

Lines 111-112. Do you mean DHA reflects the total range of oxidative activity and other activities such as catalase and β-glucosidase, and the amount of total N? This last is not correct, all these enzymes are involved in different reactions, and they are not always related with N content in soils. Please rephrase.

Line 113. DHA is an intracellular enzyme.

Lines 129-131. Considering previous lines, what about: Whether the nature of the spatial distribution of the macro- and microelements affect the microbial biomass and biochemical properties in soil?

Lines 127-128 and 134-135. Are there two objectives? Or the objective mentioned twice? As a recommendation: The detailed aim (lines 134-135) can be placed after the lines 127-128 as the detailed activities of the main objective.

Line 138. I recommend avoid direct and strong prediction according results obtained here, so, this research findings can or might be used as sensitive and effective tools for the development of precision farming.

 

Materials and methods

Comments: Were the soil samples stored at 4° (or lower) until the assessment of soil biological properties? Were the soil samples sieved?

 

Lines 151-152. Can you please provide the reference?

Line 158. “, respectively.”.

Lines 163-165. This can be avoided here, in case of keeping it, this phrase can be located in the introduction.

Line 166. I recommend focusing this section on just “Soil sampling”, which is for all determinations (physicochemical and biochemical).

Line 170. There is a missing “.” Before “In both”.

Lines 173-175. A recommendation: These analyses can be located in the section 2.5, which might include all physicochemical properties.

Lines 199-202. A recommendation: I would consider move this phrase to the Introduction since it supports the assessment of microbial biomass related to N balance.

Lines 186-202. Important: please provide references for these methods.

Line 214. As explained for soil assessments, can you briefly explain how N was measured on grains, seeds, and biomass?

Lines 219-220. The Tukey´s test is a multiple comparison test that should be applied when a previous analysis of variance (not mentioned here) is significant, which evaluates the effect of factor(s). Thus, what do you mean with “homogeneus subsets”? variance homogeneity?

Lines 220-222. As you show in results, the Pearson correlation was applied on all variables, not only on DHA vs microbial biomass. Also, did you check the data normality???

Lines 222-224. The Pearson correlation is ok to assess relationships between variables. Thus, please explain the reason of applying the PCA (e.g., to reduce the dimensionality and assess the variables that better explained the variability, to assess associations of response variables with spatial sampling points, among others).

Line 230. What type of Kriging was applied? Also, was a data transformation required? Did you found trends?

Lines 231-232. Could you please mention the packages and functions used in R? This might be useful for readers.

 

Results

Can you please provide details of models (and parameters)?

Do you have the interpolation error maps? Can you include the semivariograms as appendix?

Lines 239-241. This can be mentioned in the discussion.

Line 253 (Table 2). At this point of the manuscript many questions raised: So, a two-way ANOVA was applied??? This was not mentioned in materials and method. Please provide details about it. Also, information about factors should be explained in materials and methods. In this sense, Term is the sampling periods within each year, isn’t it? In that case, can you explain the Point factor? If there is a composite sample by each sampling point, there is only one sample by each point, which would not make possible comparison between points except if they are grouped. Please provide details about statistical design in materials and methods.

Lines 247. What maps? Please refer to Figures shown in the manuscript.

Lines 244-246. Please rephrase, the idea is unclear.

Line 247. Principal component analysis (PCA) and Pearson correlation (Table A2) showed correlations, not only PCA.

Figures 2 and 3. Both figures can be merged, showing each figure in two panels (A and B).

Section 3.1. Can you provide modelling results (Equation and parameters) for DHA?

Equations 2 and 3. Can you explain the parameters of each equation? Also, models only included DHA? In that case, what about other important variables such as TOC and pH? Can you show all equations?

Lines 288-290. Can you explain or describe the equations?

 

Discussion

 

 

Can you better explain spatial trends for DHA and microbial biomass? There are many biological references about the possible effects of the Term factor; however, within each Term, spatial trends are not discussed. This is contrasting with the discussion of N content, where the spatial trend was explained.

 

Lines 404-405. This should be mentioned in Results.

Lines 460-461. Ok, but can you explain the spatial trends? This is interesting especially when comparing the found gradients with the heterogeneous terms.

Figures 13-15. Were the normality and homoscedasticity assumptions evaluated before applying the ANOVA?

Lines 519-520. Why?

 

Line 534. By “soil reaction” do you mean pH?

 

 

Author Response

Please see the attachment.

Author Response File: Author Response.pdf

Reviewer 2 Report (New Reviewer)

Review Comments for Agronomy manuscript agronomy-1903345, entitled "Spatial and temporal variability of the microbiological and chemical properties of soils under wheat and oilseed rape cultivation", submitted by Grzyb et al. (2022).

General Comments

The authors of the manuscript dealt with the topic of the spatial and temporal variability of the microbiological (i.e., microbial biomass and dehydrogenase (DHA) enzyme activity) and chemical properties (i.e., micro- (Na, Mg, Ca) and macro-elements (Cu, Zn, Mn, Fe)) of soils under wheat and oilseed rape cultivation. This manuscript is easy to follow and generally the quality of manuscript is good in terms of writing, statistics, data presentation and discussion of the obtained results. In this case, I recommend the article for publication in the journal Agronomy after addressing the following issues.

Specific Comments

-Line 15 Why did you mention the turnover of crop residues? This may be not the focus of this study.

-Line 17 Please change ‘this research’ to ‘this study’.

-Line 19-20 Please make soil sampling depth specific.

-Line 23-25 Please quantity those effects reported in these two sentences.

-Line 28 Please add a statement of implications/ramifications of results to end the Abstract section. What do the results you obtained mean in a larger context?

-The introduction section is too long, with too many references that make little sence. It is important to identify the shortcomings of previous studies and the highlights of this study, rather than simply listing the exiting publications. Please revise the introduction section carefully.

-Line 67 Please change ‘breakdown’ to ‘decomposition’.

-Line 82 Please change ‘Classic’ to ‘Conventional’.

-Line 145 -Could you provide some clear hypotheses on your study?

-Line 151 and 152 Please add the relevant references.

-Line 160 to 163 Please add the specific mineral fertilization input rate.

-In the Discussion section, there were excessive citations regarding the findings of previous research, such as lines 584-594. Please reduce the citations of previous studies and instead strengthen to discuss the possible reasons and significance of your obtained results. In addition, the number of references in this article is a little too large (137 references). I suggest the authors to delete some references of little significance.

-From my side, the bigest issueis that there were not hypotheses in this study, I suggest the authors to provide clear hypotheses and to discuss the linkage to the proposed hypotheses in the Discussion section.

-Line 621 Please add a statement of implications/ramifications of results to end the Discussion section. What do the results you obtained mean in a larger context?

-Line 623-629 I suggest to delete this paragraph because it is not the conclusion of this study.

Author Response

Please see the attachment.

Author Response File: Author Response.pdf

Round 2

Reviewer 2 Report (New Reviewer)

Dear Editor and Authors:

After careful revision by the authors of the manuscript, I recommend that the article can be published in Agronomy. The editing of the manuscript in relation to my queries is fully satisfactory.

All the best.

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

 

In my opinion, the manuscript (Spatial and temporal diversification of biomass and activity of soil microorganisms as a precision farming tool) is interesting and drafted well. It would give information about the utilization of soil resources with respect to an understanding of microbial activity and turnover of crop residues in fields, which is an essential study to maintain soil health. The idea of the manuscript is most demandable and reasonable for managing sustainable food security. Overall the quality of the manuscript is good, but the language of the manuscript must be improved in the revised manuscript and add suitable relevant references; it can be improved further with the following suggestions-

 

1.      Introduction section is long, no need to write more details, while write critically, add correct hypothesis and correlate with objective clearly.

2.      Authors are reported about microbial activities in this work, but did not mention about species of microbes; means not molecularly identified / not submitted any sequences to gene bank and not reported any accession numbers of microbial isolates. This information is very relevant to prove microbial activity to strengthen soil and crop etc..Please clarify and add.

3.      Authors are reported huge data to support this study, why only one parameter –DHA activity chosen to prove the results, in my opinion Authors should analyzed another soil enzymatic activity including DHA and correlate this study, rather adding so much of the data. Please justify?

Further minor suggestion maybe suggest after major revision.

Thanking you

Author Response

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Author Response File: Author Response.pdf

Reviewer 2 Report

This study measured biomass, soil microbes, and chemical properties multiple times to develop a spatial and temporal guide for precision farming. The authors found that all of the parameters tested were variable in space and time. This study could help farmers determine management timing and rates based on the spatial arrangement of important soil properties.

I have a few main concerns with the manuscript, including consistency, statistics, and methods. When referring to the sampling points where the soil was collected, the authors used many different ways to refer to the sampling points, including objects, points, variants, sites, and soil collection points. Sometimes different nouns would be used in the same sentence. This was very confusing to me as a reader, and I spent a lot of time ensuring that they all meant the same thing. It would be much easier for the reader to understand the flow if a consistent word was used for the sampling points. I recommend not using variants because that made me think of different plant types or objects. After all, that made me think others things (other than the sampling points) were being tested.

In this study, the same sampling points were measured multiple times; therefore, this study could benefit from a repeated measures analysis.

I am concerned about some methods that were not reported and important soil variables that were not measured. The authors describe multiple times how important certain factors are to soil microbial populations and nutrients, including soil management, texture, pH, temperature, and moisture. For example, there are very good descriptions and citations at L414-426, L369, and L465-469 (to point out just a few). However, I find it strange that many of these important variables were not measured, or if they were, they were not described in the methods. pH and moisture are included in the PCAs but are not described in the methods or taken into effect in other places.

Finally, the title of the paper and the keywords indicate the importance of precision farming, and the study shows spatial and temporal differences. However, the discussion does not mention precision agriculture. Therefore, I think information about precision farming should be touched on in the discussion to highlight how it relates to the work done in this study.

Below are line-by-line comments and suggestions.

L118: Expand on precision agriculture and why it is important.

L128. Include the scientific names for winter wheat and winter oilseed rape.

L129. You mention that the procedures were done according to principles of good agriculture, but the readers need more details to interpret and understand the results. What was the planting rate? Were any amendments used (e.g., fertilization)? Describe the soils (e.g., soil series or at least soil order). This paper reports important soil characteristics, but it's hard to interpret the results without knowing the soil's baseline. Also, report the site's climate (e.g., average temperature and precipitation). This would be especially helpful to know this information for the time during the study.

L136-137. Change "which 1 mixed sample was made" to "and composited."

Table 1. What were the conditions during sampling (e.g., temperature, moisture, etc.)?

L147. What kind of spectrophotometer did you use?

L151. Moulds should be molds.

L160. Moulds should be molds

L 165. What elements did you measure?

L167. Delete "To" and then capitalize "two."

L169. What is the location of the Eberbach shaker?

L171. What is the location of the FAAS?

L178. This study sounds like it should be analyzed with Repeated Measures.

L183. Change between to among.

L192. Give more information about R – this is software and should be cited.

L193. Give more information about QGIS – this is software and should be cited.

L205. The use of tested enzymes implies that more than one enzyme was tested. However, only DHA was measured?

L213. Reference Figure 2 at the end of the sentence.

L214-215. Edit this table caption. The title indicates that enzyme activity is the only thing in the table, but that is not the case.

L217. Use among instead of between.

L222. At this point, dehydrogenase has already been identified as DHA; use DHA instead. This changing back and forth occurs throughout the paper.

L224. The sentence "However, in the case of rape in soil variants 48, 56-58 and 64-66" is confusing and incomplete. Is it referring to DHA? Is there a figure that goes with this?

L228. Add to the figure caption. What is going on here, what do the colors mean? What is a sample – soil collection point?

L231. Change analyzes to analysis

L234. Figure 5ab  - how do I know what is panel a or b? The figure panels are not labeled (this is a problem for all figures with multiple panels.

Figure 5 upper right-hand panel. Legend indicates III, but the caption says II.

L238. Related to the above – this is the caption that says II.

L245. Add the figure citation to the end of the sentence, so the reader knows where to look.

L258-260. Where is this information shown? Reference a figure.

L268. This figure is out of place. It should be referenced back by the other heat map.

L269-276. Where can the reader see these results?

L282-283. Where is the evidence of these changes?

L284. Change analyzes to analysis

L298. Change analyzes to analysis

L320. Change nitrogen to N.

L322. Change nitrogen to N.

L322. Delete from

L327. Put a space between of and %

L328. You mention point 41. I'm not following this on the map. On the chart, 41 is very red, indicating low N?

L330. What about the lowest at 38 and 50?

Figures 9 and 10. Were the differences significant?

L343-345. New figures do not belong in the discussion; report these in the results.

L353. Did you measure F:B? You should have the data to make this calculation.

L360. This is a good example of the importance of seasonal changes to microbes. Did you measure temperature and soil moisture?

L383. What is the scientific name for cucumber?

L391-394. This is just repeating the results. Tell us why you got the results in the discussion.

L394. Put a space between figure and 3.

L411. Did you measure pH or soil C? These are very important measures, as you indicate in this paper.

Figure 13. Make sure the graph is labeled. Add bacterial biomass to the y-axis label.

L421. Make A lowercase.

Figure 14. Make sure the graph is labeled. Add fungal biomass to the y-axis label.

L424. Make A lowercase.

L430. You refer to table A7. If this is the first mention of the appendix, it should be A1. In addition, the appendix has A3-A7; what happened to A1 and A2?

L471. Put a space between Figure 2 and Figure 3.

L477. You mention the authors' own research; are you referring to Bao et al. or this study?

L481. Change own research to this study.

L483. You mention the above-mentioned authors; are you referring to Yue et al.?

L486. Was the field in this study fertilized?

L506-508. How did you measure moisture?

L511. What % did Glowacka [111] find?

Author Response

Please see the attachment.

Author Response File: Author Response.pdf

Round 2

Reviewer 1 Report

 

The authors not revised manuscript substantially, and not address the real issue Specially my earlier comment:  Authors are reported about microbial activities in this work, but did not mention about species of microbes; means not molecularly identified / not submitted any sequences to gene bank and not reported any accession numbers of microbial isolates. This information is very relevant to prove microbial
activity to strengthen soil and crop etc..Please clarify and add. –

Authors stated very badly statement “Due to the very large amount of data, it is planned to present the issue of microbial species in another article on the soil profile and the cross- section of this research object”, real science is  more relevant rather than adding more data which is not required as per your objectives.

 

 

Author Response

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Author Response File: Author Response.pdf

Reviewer 2 Report

Thank you for making the suggested changes. Good luck with the continuing research. 

Author Response

Once again, we would like to thank the Reviewer for dedicated time and tips we received.