Micronutrients and Soil Microorganisms in the Suppression of Potato Common Scab

Round 1

Reviewer 1 Report

The authors have reviewed a large amount of significant literature. The collected data are quite well summarised in the tables. However, the text is not always sufficiently clear and sometimes highly confusing. In some cases this is caused by linguistic problems. Often wrong or ambiguous wordings are used. But also often (partially) false conclusions are drawn. Moreover, it is often not clear which are conclusions or summaries from the authors themselves, or when conclusions from cited literature are echoed. Below an anthology is provided of only a few points that need improvement. I recommend that the authors further scrutinise the entire manuscript, to solve problems as outlined above

Line 10: Nature-sensitive approaches

• Do you mean nature inclusive?

Line 35: Thus, a composed plant nutrition is critical for disease control because that is responsible for a delicate balance between the plant’s genetics and environment [7–12].

• This sentence does not logically follow from the previous sentence. Especially the plant genetics part deserves further introduction.

Line 41: Currently it was suggested

• Recently it was suggested OR currently it is suggested. Two of three cited references date from 2010, which is not very current or recent.

Line 44: Common scab of potatoes (CS) caused by pathogenic Streptomyces spp., belongs among diseases, which are affected by plant mineral nutrients

• … belongs to diseases that are … OR … is an example of a disease that is …

Line 54: We focus on the effects of micronutrients, which represent physiological processes supporting the defense against plant diseases and are relatively easy to manage.

• How micronutrients represent physiological processes? Or do you mean trigger instead of represent?

Line 56: microorganisms are inevitable components of soils

• Do you mean inevitable? or indigenous

Line 66: ….only certain interactions are indicative of CS….

• What do you mean by certain interactions? Or do you mean some interactions?

In the sections headed by nutrient names it is often not clear when you mean ionic free, bound, or elementary nutrients. Try to specify this as much as possible.

Line 82: Therefore at low Ca, cell walls leak low molecular weight organic compounds, which are used as a substrate by CS pathogens.

• Has it been shown that Ca depletion indeed causes leakage of cellulose derivatives? And that calcium depletion, successively, results in enhanced growth of Ss? References are missing

Line 83: Also, Ca serves as a second messenger triggered by different environmental stimuli, including the pathogens so it is needed for plant defense [37].

• Ca2+ serves as second messenger inside plant cells indeed. But Ca in the soil does not affect intracellular signalling. The authors are confusing two completely different concepts here.

Line 87: … streptomycetes, stimulate H+ efflux across the cell membrane and a short-lived Ca2+ influx to plant roots [41,42]. That leads to elevated Ca levels in CS lesions…

• Again the authors confuse intracellular signalling with extracellular Ca accumulation. When Ca levels are measured in lesions, primarily the cellwall bound calcium is measured. This concentration is several orders of magnitudes higher than intracellular calcium. So, the point the authors try to make is invalid.

Line 119: In contrast, the numbers of thaxtomin gene copies (txtB) in potato periderm were found positively correlated to periderm Mg content.

• This is a confusing sentence. Why is it contrasting with the previous sentence? txtB was used to quantify bacteria in the tuber. It was found that higher numbers of bacteria correlated with higher the magnesium concentrations. If a variety has a high magnesium concentration it does not necessarily mean that it has a high amount of bacteria. So, high magnesium concentration alone cannot account for the resistance of the variety Kariera.

Line 303: In another study, the number of thaxtomin gene (txtB) copies was positively correlated with the soil C and N contents showing that the quality of SOM is directly related to the disease [29]. That is supported by evidence that some carbohydrates may act as environmental signals to plant pathogenic Streptomyces allowing the production of thaxtomin [116].

> several fundamentally different and unrelated aspects are mixed here, resulting a very confusing text.

1. txtB is used to quantify the bacteria. It is highly unusual to mention the gene that was used in Q-PCR to quantify the bacteria.
2. How can a vague description like “quality of SOM” be directly correlated with something. A direct correlation can only be shown with defined components.
3. Some carbohydrates… Please specify
4. Allowing? Or inducing?
5. There is no connection between the txtB accumulation induced by C and N content in the first sentence, and the induction of taxtomin synthesis by cellubiose

Line 306: Also, these carbon compounds increase their competitiveness

• Specify which carbon compounds you mean. Are these carbon compound present in compost and manure?

Line 307: quality of organic compounds,

• Quality is to ambiguous and requires specification

Line 314: which most closely reflects to the balanced state between limiting nutrients, carbon sources and microbial activities.

• This is an extremely vague statement, please clarify.

Line 315: Generally, organic matter supplements containing small sugars should be avoided, while fresh low pH SOM will help in nutrient release and older more decomposed SOM will

benefit activities of antagonistic streptomycetes.

• This is a clear statement. Is it your own conclusion from the references that you describe in the previous part of this section? Then please state that it is you conclusion. Otherwise provide a reference.

Line 320:  agoecosystems.

Line 340: which are families of known plant growth promoting activities

• which are families of known plant growth promoting microbes

Line 346: However, bottom-up control although it is certainly crucial, represents only half of the story because microorganisms are subjected to the top-down control by a range of bacterial and eukaryotic consumers.

• This is a confusing sentence. Clarify what you mean and provide references.

Line 366: which points to the changes in soil pH and nitrogen metabolism [25].

• This is a confusing and inaccurate statement

Line 370: In contrast, the tuberosphere of a susceptible cultivar was enriched in Variovorax, Stenotrophomonas, and Agrobacterium together with several ABC transporter genes, genes of bacterial secretion system, quorum sensing, cytochrome P450 but also nitrogen metabolism [14], which again suggests that exchange of compounds between soil and plants, together with microbial community interactions and nitrogen related process are important in CS disease control (Fig.1, Table 3).

• This is so confusing. Occurrence of bacterial species, expression of host and pathogen genes are taken together in one sentence to argue for a role of component exchange between soil and plant. And moreover a very confusing conclusion is drawn ion the last part of the sentence. A review paper is meant to sort and clarify information from literature, not to obscure it.

Author Response

Open Review

 (x) Moderate English changes required

English was edited by two native English speakers.

Comments and Suggestions for Authors

The authors have reviewed a large amount of significant literature. The collected data are quite well summarised in the tables. However, the text is not always sufficiently clear and sometimes highly confusing. In some cases this is caused by linguistic problems. Often wrong or ambiguous wordings are used. But also often (partially) false conclusions are drawn. Moreover, it is often not clear which are conclusions or summaries from the authors themselves, or when conclusions from cited literature are echoed. Below an anthology is provided of only a few points that need improvement. I recommend that the authors further scrutinize the entire manuscript, to solve problems as outlined above.

Dear Reviewer,

Thank you for the comments and corrections. We appreciate your work very much and we tried to accommodate all recommendations as well as we could. Hopefully, you will find the MS improved.

Yours sincerely, Marketa Sagova-Mareckova

Line 10: Nature-sensitive approach

• Do you mean nature inclusive?

Modified to Nature-friendly. L 10

Line 35: Thus, a composed plant nutrition is critical for disease control because that is responsible for a delicate balance between the plant’s genetics and environment [7–12].

• This sentence does not logically follow from the previous sentence. Especially the plant genetics part deserves further introduction.

The sentence was divided and modified. “Plant genetics” was omitted from the explanation.   L 37-40

Line 41: Currently it was suggested

• Recently it was suggested OR currently it is suggested. Two of three cited references date from 2010, which is not very current or recent.

Corrected. The beginning of the sentence was omitted. L 47-48

Line 44: Common scab of potatoes (CS) caused by pathogenic Streptomyces spp., belongs among diseases, which are affected by plant mineral nutrients

• … belongs to diseases that are … OR … is an example of a disease that is …

The whole sentence is changed and part of the sentence was omitted. L 49-50

Line 54: We focus on the effects of micronutrients, which represent physiological processes supporting the defense against plant diseases and are relatively easy to manage.

• How micronutrients represent physiological processes? Or do you mean trigger instead of represent?

Modified to “sufficient amount is required for many physiological processes”. L 59-60

Line 56: microorganisms are inevitable components of soils

• Do you mean inevitable? or indigenous

Changed to “integral”. L 62

Line 66: ….only certain interactions are indicative of CS….

• What do you mean by certain interactions? Or do you mean some interactions?

Changed to “some”. L 72

In the sections headed by nutrient names it is often not clear when you mean ionic free, bound, or elementary nutrients. Try to specify this as much as possible. 

Added to places, where it was possible. E.g. L 76, L 79-80, L 110, L 118, L 135 (Please see in TrackedChanges)

Line 82: Therefore at low Ca, cell walls leak low molecular weight organic compounds, which are used as a substrate by CS pathogens.

• Has it been shown that Ca depletion indeed causes leakage of cellulose derivatives? And that calcium depletion, successively, results in enhanced growth of Ss? References are missing.

 The sentence was omitted and the whole paragraph about Ca was modified. L 87-92

Line 83: Also, Ca serves as a second messenger triggered by different environmental stimuli, including the pathogens so it is needed for plant defense [37].

• Ca2+ serves as second messenger inside plant cells indeed. But Ca in the soil does not affect intracellular signalling. The authors are confusing two completely different concepts here.

Yes. The sentences were confusing. The information was not meant to be comparable. Now, it was modified just to show what for is calcium in the plant. We tried to write it more clearly.

Line 87: … streptomycetes, stimulate H+ efflux across the cell membrane and a short-lived Ca2+ influx to plant roots [41,42]. That leads to elevated Ca levels in CS lesions…

• Again the authors confuse intracellular signalling with extracellular Ca accumulation. When Ca levels are measured in lesions, primarily the cell wall bound calcium is measured. This concentration is several orders of magnitudes higher than intracellular calcium. So, the point the authors try to make is invalid.

Yes. This statements was omitted. We modified the paragraph.

Line 119: In contrast, the numbers of thaxtomin gene copies (txtB) in potato periderm were found positively correlated to periderm Mg content.

• This is a confusing sentence. Why is it contrasting with the previous sentence? txtB was used to quantify bacteria in the tuber. It was found that higher numbers of bacteria correlated with higher the magnesium concentrations. If a variety has a high magnesium concentration it does not necessarily mean that it has a high amount of bacteria. So, high magnesium concentration alone cannot account for the resistance of the variety Kariera.
• It was modified and “in contrast” was omitted. L 120-122

Line 303: In another study, the number of thaxtomin gene (txtB) copies was positively correlated with the soil C and N contents showing that the quality of SOM is directly related to the disease [29]. That is supported by evidence that some carbohydrates may act as environmental signals to plant pathogenic Streptomyces allowing the production of thaxtomin [116].

> several fundamentally different and unrelated aspects are mixed here, resulting a very confusing text.

1. txtB is used to quantify the bacteria. It is highly unusual to mention the gene that was used in Q-PCR to quantify the bacteria.

Yes, we are aware that in literature concerning agriculture and also environmental sciences and similar applied research areas, no gene names used for diversity or quantification assessments are mentioned, they are rather called markers or barcodes. Thus, we exchanged the gene txtB for “pathogen” as it is used to quantify the pathogens using txtB gene from the thaxtomin biosynthetic pathway. In microbiology, the genes are always named even in case of 16S rRNA gene, which is the most common marker. It is quite important because the specificity of detection is dependent upon the gene used and it is needed for comparison with results obtained by other genes.

How can a vague description like “quality of SOM” be directly correlated with something. A direct correlation can only be shown with defined components.

Yes, we agree. “Direct” was a strong word to just propose a general connection. The sentence was reworded.

1. Some carbohydrates… Please specify

Explained in detail L 309-315

1. Allowing? Or inducing?

Yes. Changed.

1. There is no connection between the txtB accumulation induced by C and N content in the first sentence, and the induction of taxtomin synthesis by cellubiose.

The paragraph was divided to two parts and explained. L 304-308; L309-315

Line 306: Also, these carbon compounds increase their competitiveness

• Specify which carbon compounds you mean. Are these carbon compound present in compost and manure?
• Yes, that is what we meant that these are various compounds present in compost and manure. We reworded the paragraph.

Line 307: quality of organic compounds,

• Quality is to ambiguous and requires specification

Line 314: which most closely reflects to the balanced state between limiting nutrients, carbon sources and microbial activities.

• This is an extremely vague statement, please clarify.
• The sentence was omitted. The paragraph was modified L 316-321

Line 315: Generally, organic matter supplements containing small sugars should be avoided, while fresh low pH SOM will help in nutrient release and older more decomposed SOM will benefit activities of antagonistic streptomycetes.

• This is a clear statement. Is it your own conclusion from the references that you describe in the previous part of this section? Then please state that it is you conclusion. Otherwise provide a reference.

The sentence was modified to clarify that it was our conclusion.

Line 320:  agoecosystems.

Corrected

Line 340: which are families of known plant growth promoting activities

• which are families of known plant growth promoting microbes

Corrected. L 342

Line 346: However, bottom-up control although it is certainly crucial, represents only half of the story because microorganisms are subjected to the top-down control by a range of bacterial and eukaryotic consumers.

• This is a confusing sentence. Clarify what you mean and provide references.

The paragraph was reworded to improve the flow of the text. L 346-349

Line 366: which points to the changes in soil pH and nitrogen metabolism [25].

• This is a confusing and inaccurate statement.

Explained in more detail. References added. L363-365

Line 370: In contrast, the tuberosphere of a susceptible cultivar was enriched in Variovorax, Stenotrophomonas, and Agrobacterium together with several ABC transporter genes, genes of bacterial secretion system, quorum sensing, cytochrome P450 but also nitrogen metabolism [14], which again suggests that exchange of compounds between soil and plants, together with microbial community interactions and nitrogen related process are important in CS disease control (Fig.1, Table 3).

• This is so confusing. Occurrence of bacterial species, expression of host and pathogen genes are taken together in one sentence to argue for a role of component exchange between soil and plant. And moreover a very confusing conclusion is drawn ion the last part of the sentence. A review paper is meant to sort and clarify information from literature, not to obscure it.

This is a summary of important results of one publication. The paragraph was reworded to make it clearer. L 370-375

Reviewer 2 Report

This is an exhaustive and well-documented review on the effects of micronutrients and microorganisms in suppressing potato common scab. The examples cited are clear and the data well presented. I am confident that this review will be an interesting and updated reference for a specialist audience in this field of work. I recommend this review for publication once minor typos and edits have been performed.

Author Response

Thank you for the review. The English was corrected by two native English speakers. 

Reviewer 3 Report

The comments and suggestions for the manuscript entitled "Micronutrients and microorganisms in the suppression of potato common scab."(Manuscript ID: agronomy-1087622) are appended below-

1. Abstract: Line no-21 to 24. It is unclear what authors wish to convey by this sentence (L.No21 to 24). Please reframe it to a more comprehensible sentence.
2. Introduction- Authors have started the abstract with a gap in research describing no available strategies for CS management and reduction of chemical pesticide as a goal, however, there is no mention of any research gap in the introduction section. I suggest authors must include some sentences for problems of chemical pesticide uses and gap existence in management strategies. It is not much clearer with the introduction section. I strongly suggest to work and improve the same.  
3. Section 3. Organic matter modifies microbial communities and increases antibiosis: Line no-265- the authors have included specific crop rotations as a suppressive mechanism for CS in potato. I suggest either remove this from the section or add another subheading and describe crop rotations or cover crop in details (Ex- https://doi.org/10.1094/PDIS-03-10-0172), and impact of cover crop and green manure combined, as crop rotation does not fit in Section 3 which is dedicated to organic matter and mechanism.
4. Line no 320- cycling in agoecosystems. I guess there is a typographical error and it must be agroecosystems.
5. I suggest Section 6. Subheading Conclusions are enough please remove for CS management.
6. Conclusion- I suggest to work on the conclusion section and make it more concise and concreate with what authors have addressed and how it will be beneficial in future research. 

Author Response

Dear Reviewer,

We would like to thank you for corrections and suggestions. MSM

Open Review

(x) I would not like to sign my review report

( ) I would like to sign my review report

English language and style

( ) Extensive editing of English language and style required

( ) Moderate English changes required

(x) English language and style are fine/minor spell check required

English was edited by to native English speakers.

         Comments and Suggestions for Authors

The comments and suggestions for the manuscript entitled "Micronutrients and microorganisms in the suppression of potato common scab."(Manuscript ID: agronomy-1087622) are appended below-

Abstract: Line no-21 to 24. It is unclear what authors wish to convey by this sentence (L.No21 to 24). Please reframe it to a more comprehensible sentence.

Corrected. L 21-22

Introduction- Authors have started the abstract with a gap in research describing no available strategies for CS management and reduction of chemical pesticide as a goal, however, there is no mention of any research gap in the introduction section. I suggest authors must include some sentences for problems of chemical pesticide uses and gap existence in management strategies. It is not much clearer with the introduction section. I strongly suggest to work and improve the same. 

Several sentences concerning not only pesticides but also other agrochemicals were added. L 27-31, L 50-52

Section 3. Organic matter modifies microbial communities and increases antibiosis: Line no-265- the authors have included specific crop rotations as a suppressive mechanism for CS in potato. I suggest either remove this from the section or add another subheading and describe crop rotations or cover crop in details (Ex- https://doi.org/10.1094/PDIS-03-10-0172), and impact of cover crop and green manure combined, as crop rotation does not fit in Section 3 which is dedicated to organic matter and mechanism.

Notes on crop rotations were removed.

Line no 320- cycling in agoecosystems. I guess there is a typographical error and it must be agroecosystems.

Corrected.

I suggest Section 6. Subheading Conclusions are enough please remove for CS management.

Done.

Conclusion- I suggest to work on the conclusion section and make it more concise and concreate with what authors have addressed and how it will be beneficial in future research.

Modifications to the section were done to strengthen the conclusions.