Fertilization and Soil Microbial Community: A Review

Round 1

Reviewer 1 Report

I'd suggest re-organizing the paper such that a description of organic fertilizers currently found at the end is moved to the beginning. Please add a definition of chemical fertilizers as well at the beginning to clarify the differences between chemical, organic and mineral fertilizers. Please edit carefully as there are grammatical and English language errors. Please ensure that there are citations where needed. For example, there should be a citation in line 46 "only 25% of P applied is taken into plants." I'd suggest adding a Discussion or Implications or Significance section prior to Conclusions where you address how the review findings come together and what do they mean. Many times throughout the paper, a finding is stated but not explained or discussed leading the paper to lack depth and clarity. For example, line 130 states that "Long-term NPK applications was found to result in organic matter loss." Please explain why that is and why that matters- what is the significance of this? How does it relate to the theme of the review -- how fertilizers affect the soil microbial community? Always link back to how the finding affects the microbial community. Other times, terms should be briefly defined or given context. For example, line 146 says that dehydrogenase activity is affected by NPK fertilization- what is dehydrogenase, which species produce it, and why does it matter? What is the relationship between soil microbial communities and microbial biomass and plant growth? Line 241- why is Azotobacter the most representative bacteria? 297- Fungi and enzymes --- this is not clear. Do you mean the enzymes produced by fungi? Overall I would suggest reorganizing the paper for clarity and adding depth and focus - the paper currently does not clearly address it's stated objective and does not clearly describe the significance of the findings or discuss implications adequately, rather lists findings from the literature. At the end, plant growth promoting microorganisms are mentioned in the last sentence that have not been defined or discussed in the paper. Claims are made in the conclusions that are unsupported by citations or discussion in the review, such as "Because it is not reasonable possible use only organic amendments to support plant productivity, a combine addition of chemical and organic fertilization could be a right 
way, particularly for soils with low N, P, and organic C contents." 363 (Also note the English errors in this sentence).

Author Response

I'd suggest re-organizing the paper such that a description of organic fertilizers currently found at the end is moved to the beginning. Please add a definition of chemical fertilizers as well at the beginning to clarify the differences between chemical, organic and mineral fertilizers.

Thank you for your suggestion. We have added the definition of chemical and organic fertilizers in the introduction. Moreover, a list of main organic fertilizers is reported in a new Table 1.

Please edit carefully as there are grammatical and English language errors.

Thank you. A person of English mother tongue revised the manuscript and several improvents were made in all the text.

Please ensure that there are citations where needed. For example, there should be a citation in line 46 "only 25% of P applied is taken into plants."

Thank you for your comment. We have added several references where they were needed (see references in yellow in the text).

I'd suggest adding a Discussion or Implications or Significance section prior to Conclusions where you address how the review findings come together and what do they mean.

Thank you for your comment. Since the manuscript was substantially improved by adding in each section a discussion of different aspects of chemical and organic fertilization, we did not added another section.

Many times throughout the paper, a finding is stated but not explained or discussed leading the paper to lack depth and clarity. For example, line 130 states that "Long-term NPK applications was found to result in organic matter loss." Please explain why that is and why that matters- what is the significance of this? How does it relate to the theme of the review -- how fertilizers affect the soil microbial community? Always link back to how the finding affects the microbial community.

Thank you for your suggestion. We have improved the manuscript in several parts and several additional references were added. The authors are confident that now the manuscript is more explicative.

Other times, terms should be briefly defined or given context. For example, line 146 says that dehydrogenase activity is affected by NPK fertilization- what is dehydrogenase, which species produce it, and why does it matter?

Thank you for your question. We have specified dehydrogenase activity and how it is affected by different fertilizations.

What is the relationship between soil microbial communities and microbial biomass and plant growth?

Thank you for your question. Soil microbial communities have a key role in multiple ecosystem functioning, and a diverse and abundant microbial community is an index of a good soil quality. The latter is a pre-requisite for plant grow and, consequently, for crop production. We have explain it better in the introduction.

Line 241- why is Azotobacter the most representative bacteria?

Thank you for your question. Azotobacter is a free-living, nitrogen fixing aerobic soil bacteria able to make available to plants a considerable part of soil nitrogen. We have add this sentence in the text with an updated reference (Sumbul, A.; Ansari, R.A.; Rizvi, R.; Mahmood, I. Azotobacter: A potential bio-fertilizer for soil and plant health management. Saudi J. Biol. Sci. 2020, 27, 3634–3640).

297- Fungi and enzymes --- this is not clear. Do you mean the enzymes produced by fungi?

Thank you for your question. Yes, we have corrected it in the text.

Overall I would suggest reorganizing the paper for clarity and adding depth and focus - the paper currently does not clearly address it's stated objective and does not clearly describe the significance of the findings or discuss implications adequately, rather lists findings from the literature.

Thank you for your comment. We have substantially improved the main text and the conclusion section.

At the end, plant growth promoting microorganisms are mentioned in the last sentence that have not been defined or discussed in the paper.

Thank you for your comment. In the new Table 1, the plant growth promoting microorganisms are reported and also in other parts of the text.

Claims are made in the conclusions that are unsupported by citations or discussion in the review, such as "Because it is not reasonable possible use only organic amendments to support plant productivity, a combine addition of chemical and organic fertilization could be a right way, particularly for soils with low N, P, and organic C contents." 363 (Also note the English errors in this sentence).

Thank you for your comment. Normally the conclusions do not need citations, as they are conclusions and not discussions. The sentence you mentioned is also already supported in the main text in the discussion section in several parts.

Reviewer 2 Report

The Authors address a very interesting and timely subject in a very interesting way. It is original (in the present context) to ask how mineral fertilization may contribute to soil biodiversity. However I think that there is still a lot of work that needs to be performed before the work can be accepted for publication.

My main concerns relate with the way the Authors implemented their idea.

Examples:

The part of the introduction dealing with "mineral fertilization" needs to be revisited. NPK are essential nutrients and this concept is not present in the text.

The "materials and methods" section creates the expectation of a systematic review, and when the papers selected for revision were divided by continent, one expects to find some relation between the content of the revision and geographical specificities. But this does not happen.

This section is not clear about the methods used to select the corpus of the revision: which platforms were searched for, what were the precise words searched, which tools were used to make the search, when was it performed, what were the inclusion and exclusion criteria, etc????

So, some more information is necessary on the description of the methodology used.

 

Concerning the "Results and discussion" section I do not understand its relation with the  papers selected for revision, which needs to be clarified.

I think the discussion itself needs structure. In its present form the reader can not have the roadmap of the discussion and it appears that one sentence is contradicting the next one, just because new variables are being introduced in the analyses (pH, fertility, organic matter content, etc.)

I would like that the Authors take my comments as an incentive to improve the manuscript and explore the excellent idea they had. But in its present form I can not recommend it for publication

 

Author Response

The Authors address a very interesting and timely subject in a very interesting way. It is original (in the present context) to ask how mineral fertilization may contribute to soil biodiversity. However I think that there is still a lot of work that needs to be performed before the work can be accepted for publication. My main concerns relate with the way the Authors implemented their idea. Examples: The part of the introduction dealing with "mineral fertilization" needs to be revisited. NPK are essential nutrients and this concept is not present in the text.

Thank you for your comment. We have substantially improved the introduction, adding several parts referred to inorganic and organic fertilizers.

The "materials and methods" section creates the expectation of a systematic review, and when the papers selected for revision were divided by continent, one expects to find some relation between the content of the revision and geographical specificities. But this does not happen.

Thank you for your comment. We have substantially improved the materials and method section, and explain why we did not reported the results divided by Countries at the start of the Results and discussion section.

This section is not clear about the methods used to select the corpus of the revision: which platforms were searched for, what were the precise words searched, which tools were used to make the search, when was it performed, what were the inclusion and exclusion criteria, etc???? So, some more information is necessary on the description of the methodology used.

Thank you for your comment. We have substantially improved the materials and method section, including the keywords searched and the tools used. The authors hope that now this section is exhaustive.

Concerning the "Results and discussion" section I do not understand its relation with the  papers selected for revision, which needs to be clarified.

Thank you for your comment. As already said, the Materials and methods and the Results and discussion sections were substantially improved.

I think the discussion itself needs structure. In its present form the reader can not have the roadmap of the discussion and it appears that one sentence is contradicting the next one, just because new variables are being introduced in the analyses (pH, fertility, organic matter content, etc.).

Thank you for your suggestion. Each sub-paragraph of the results and discussion was improved and some new findings are now inserted. The authors hope that now this core part of the manuscript is more explicative. 

I would like that the Authors take my comments as an incentive to improve the manuscript and explore the excellent idea they had. But in its present form I can not recommend it for publication

Thank you for your comment. We have taken into consideration all the reviewer’s comments.

Reviewer 3 Report

This manuscript collected a large number of data from articles published, and analyzed and summarized the effect of fertilization on soil microbial community, it is a valuable paper for researchers who study the relationship between fertilization and soil ecology, and some minor revisions are needed before publishment.

1. the title is not consistent with the content of this manuscript, title is : chemical fertilizer and soil microbial community, but in manuscript, the effect of chemical fertilizer, organic fertilizer all are evaluated, as a suggestion, “fertilization and soil microbial community ” maybe be more appropriate.
2. line 130-131. “Long-term NPK applications was found to result in organic matter loss”, this statement is not comprehensive, some studies indicated that NPK increased SOM, because fertilization increase stubble and root residue, and NPK increased SOM under crop residue returning,
3. The conclusion is too long, and the first paragraph is not necessary, it should be compressed and shorten.

Author Response

This manuscript collected a large number of data from articles published, and analyzed and summarized the effect of fertilization on soil microbial community, it is a valuable paper for researchers who study the relationship between fertilization and soil ecology, and some minor revisions are needed before publishment.

1. the title is not consistent with the content of this manuscript, title is : chemical fertilizer and soil microbial community, but in manuscript, the effect of chemical fertilizer, organic fertilizer all are evaluated, as a suggestion, “fertilization and soil microbial community ” maybe be more appropriate.

Thank you for your suggestion. You are right. The title was modified as you suggested.

2. line 130-131. “Long-term NPK applications was found to result in organic matter loss”, this statement is not comprehensive, some studies indicated that NPK increased SOM, because fertilization increase stubble and root residue, and NPK increased SOM under crop residue returning,

Thank you for your comment. This part (and also other parts, following the other reviewers’ comments) were substantially improved.

3. The conclusion is too long, and the first paragraph is not necessary, it should be compressed and shorten.

Thank you for your comment. Really being a review paper that considered inorganic and organic fertilizers, Conclusions section has the ambition to report the take-home-messages. The authors are confident that, in this form, the conclusions are fully and definitely informative.

Round 2

Reviewer 1 Report

Good job with the revisions! This is much improved and a great paper. 

Author Response

Thank you for your comment!

Reviewer 2 Report

The Authors made an effort to clarify most of the questions addressed in the revision process. However, I am still a bit confused about the methodology used to make this review.From the materials and methods I understand that this is a review of reviews. Is this so? If the authors aim at doing a systematic review we need to have a more detailed description of the materials and methods.

I am not an English native speaker, but I think the English needs to be revised.

Please replace the sentences "Chemical fertilizers (called also mineral, inorganic or synthetic fertilizers) are contain a high concentration in a primary nutrient (nitrogen, N; potassium, K; phosphorous, P) as an inorganic salt or a combination of two or three of them. Complex fertilizers can also contain secondary elements (calcium, magnesium and sulfur). Micronutrients (boron, manganese, iron, zinc, copper, molybdenum, cobalt, chlorine) [3] are in general absent in NPK chemical fertilizers and can be supplied by specific expensive synthetic fertilizers by soil or foliar applications [4]. Chemical fertilizers are produced by extraction from rocks and/or physical processes and chemical reactions" by something like:

"Chemical fertilizers (natural or synthetic ) contain a high concentration of primary (nitrogen, N; potassium, K; phosphorous, P) or secondary macronutrients (calcium, magnesium and sulphur). Micronutrients (boron, manganese, iron, zinc, copper, molybdenum, cobalt, chlorine) [3] are in general absent in NPK chemical fertilizers and constitute another type of fertilizers, usually more complex and expensive [4]. The majority of the inorganic fertilizers (with the exception of N) is extracted from rocks using physical or chemical processes"

 

Please in the sentence: "For example, N fertilizers (mainly as ammonium - NH4+ and nitrate - NO3-: urea, urea ammonium nitrate, ammonium nitrate and calcium ammo-..."

CUT ""For example,"

 

In the paragraph "Fertilizers and amending materials are regulated in the EU by Reg. 2019/1009. In the US, they are regulated at the state level rather than by the Federal Government" Please had how it is regulated in other geographical areas such as Chin, Brazil or India.

 

Can I conclude from the sentence "with state-of-the- art knowledge of the effects of long term fertilization on soil microorganisms in literature
reviews, scoping reviews and systematic reviews" that the authors are performing a review of reviews? Can the Authors explain the need for this?In the Materials and Methods section we also need the number of articles obtained, reviewed and rejected.

Please add!

 

Author Response

The Authors made an effort to clarify most of the questions addressed in the revision process. However, I am still a bit confused about the methodology used to make this review. From the materials and methods I understand that this is a review of reviews. Is this so? If the authors aim at doing a systematic review we need to have a more detailed description of the materials and methods.

Thank you for your comment. The aim of the manuscript was to revise the main up-to-date and relevant papers (not only reviews) regarding the effects of chemical fertilizers on the microbial community of soil, in particular referring to control soils (not fertilized) or soil fertilized with organic amendments.

We have explain better in material and methods as follows:

“This review considers articles published between 1990 and 2022 regarding the effects on soil microorganisms of chemical fertilization in long-term field experiments, in particular with reference to control soils (not fertilized) or soil fertilized with organic amendments. The articles were both original studies and literature reviews, scoping reviews and systematic reviews with state-of-the-art knowledge of the topic [69]. To find the main relevant studies, ERIC (Education Resources Information Center) was used together with numerous databases, including Web of Science, Science Direct, SpringerLink and Google Academic. The primary keywords used in the different databases were: use of chemical fertilizers, influence of phosphorus on soil bacteria, fertilizers and soil microorganisms, soil bacteria affected by fertilizers, long-term fertilization effects on soil microorganisms, ecological consequences of the fertilizers, and combined fertilization.

The criteria used in this review for searching articles were:

-        type of publications (only original studies or reviews were considered);

-        the main direction of the systematic review consisted in reviewing the fertilizer types and fertilizer treatments used in different countries of the world;

-        effects of chemical fertilizer management on soil microorganisms in agroecosystems across the world, also compared with organic fertilization;

-        influence of intensive and/or long fertilization on the numbers and activities of microbial communities in soils;

-        comparison between the various fertilizer regimes and their effects on soil microorganisms.

Exclusion criteria consisted in:

-        editorials;

-        studies published in a language other than English:

-        studies in specific extreme areas (e.g., arctic or arid soils).

In Figure 1 a sketch containing the methodology steps used is presented.”

 

I am not an English native speaker, but I think the English needs to be revised.

Thank you for your observation. As already mentioned, the manuscript was revised by an English mother tongue. He revised another time the manuscript and it is now again improved. I also attached the certification.

Please replace the sentences "Chemical fertilizers (called also mineral, inorganic or synthetic fertilizers) are contain a high concentration in a primary nutrient (nitrogen, N; potassium, K; phosphorous, P) as an inorganic salt or a combination of two or three of them. Complex fertilizers can also contain secondary elements (calcium, magnesium and sulfur). Micronutrients (boron, manganese, iron, zinc, copper, molybdenum, cobalt, chlorine) [3] are in general absent in NPK chemical fertilizers and can be supplied by specific expensive synthetic fertilizers by soil or foliar applications [4]. Chemical fertilizers are produced by extraction from rocks and/or physical processes and chemical reactions" by something like:

"Chemical fertilizers (natural or synthetic ) contain a high concentration of primary (nitrogen, N; potassium, K; phosphorous, P) or secondary macronutrients (calcium, magnesium and sulphur). Micronutrients (boron, manganese, iron, zinc, copper, molybdenum, cobalt, chlorine) [3] are in general absent in NPK chemical fertilizers and constitute another type of fertilizers, usually more complex and expensive [4]. The majority of the inorganic fertilizers (with the exception of N) is extracted from rocks using physical or chemical processes"

Thank you for your observation. The new sentences are as follows:

Chemical fertilizers (also termed mineral, inorganic or synthetic fertilizers) contain a high concentration of a primary nutrient (nitrogen, N; potassium, K; phosphorous, P) as inorganic salts. Secondary elements (calcium, magnesium and sulfur) can also added to soil by chemical fertilizers. Micronutrients (boron, manganese, iron, zinc, copper, molybdenum, cobalt, chlorine) [3] are in general absent in NPK chemical fertilizers and can be supplied by specific expensive synthetic fertilizers with soil or foliar applications [4].

The majority of the inorganic fertilizers (with the exception of N) is extracted from rocks using physical or chemical processes.

 

Please in the sentence: "For example, N fertilizers (mainly as ammonium - NH4+ and nitrate - NO3-: urea, urea ammonium nitrate, ammonium nitrate and calcium ammo-..."

CUT ""For example,"

 OK, done

In the paragraph "Fertilizers and amending materials are regulated in the EU by Reg. 2019/1009. In the US, they are regulated at the state level rather than by the Federal Government" Please had how it is regulated in other geographical areas such as Chin, Brazil or India.

Thank you we have added this information in the Introduction section.

Can I conclude from the sentence "with state-of-the- art knowledge of the effects of long term fertilization on soil microorganisms in literature reviews, scoping reviews and systematic reviews" that the authors are performing a review of reviews? Can the Authors explain the need for this?

Thank you for your question. As above mentioned, we have explain better in M&M section:

The articles were both original studies and literature reviews, scoping reviews and systematic reviews with state-of-the-art knowledge of the topic

In the Materials and Methods section we also need the number of articles obtained, reviewed and rejected.

Please add!

Thank you for your observation. In the Table 2 the number of the papers considered are listed. The first sentence of the Results and Discussion was improved as follows:

Overall, a total of 52 articles were considered (Table 2).