Microbiota Management for Effective Disease Suppression: A Systematic Comparison between Soil and Mammals Gut
Round 1
Reviewer 1 Report
Dear authors,
The manuscript is original and will contribute to strengthening knowledge of the role of microbiota in suppressing the use of antibiotics in organisms and of chemicals and pesticides in the soil. The article should be published after reviewing minor corrections.
382-383 : What's the plants source of the biochar? mention it.
506-507 : What would be the effect of specific suppression transfer on Rhizobacteria, Could it have harmful effects?
511-517 : In terms of energy or labor, soil transplantation can be a constrain, and therefore less efficient. Do you think she is really realistic or simple technology?
Author Response
Reviewer #1
The manuscript is original and will contribute to strengthening knowledge of the role of microbiota in suppressing the use of antibiotics in organisms and of chemicals and pesticides in the soil. The article should be published after reviewing minor corrections.
The authors would like to thank the reviewer for his dedicated time in to analyse carefully the manuscript and for his valuable comments. Efforts were made in order to improve the manuscript following the reviewer’s recommendations.
Point 1: 382-383: What's the plants source of the biochar? Mention it.
Done. The source of the biochar was indicated as follows: “In fact, specific combinations of biochar, made from four feedstocks i.e. organic fraction of municipal waste, Medicago sativa hay, Zea mays stalks, and wood chips, with not-pyrogenic substrates have been found to be very effective in stimulating plant growth” (Lines 382-384).
Point 2: 506-507: What would be the effect of specific suppression transfer on Rhizobacteria? Could it have harmful effects?
Done. Specific suppression transfer, by transferring soil and the associated microbiota, indeed affect native rhizobacteria. Unfortunately, most of studies focus on pathogens and on few key taxa with a limited number of studies that investigated the impact overall microbiota associate with plant roots. This indeed would be a key point for future research. We highlighted this point in the new version as follows: “However, because of the very limited knowledge concerning the traits of donor soil microbiota and their compatibility with recipient soils, no reliable guidelines are currently available for farmers. Moreover, future studies would investigate the impact of soil transplant on diversity and functionality of recipient microbiota”.
Point 3: 511-517: In terms of energy or labor, soil transplantation can be a constrain, and therefore less efficient. Do you think she is really realistic or simple technology?
We dedicate a complete section of this point, highlighting that transplant of 10% of soil would be not practically feasible. Instead, in case of nursery or flower cultivations in greenhouses, the surface occupied is much less than open fields, so when applying the soil transplantation, the amount that we will use is very small giving that the approach consists of using only 1% of donor suppressive soil. Moreover, in terms of energy and labour, 1% application is not prohibitive because farmers use similar amounts for applying organic amendments to their soils. Therefore, applying this amount to ensure a healthy soil with higher yield is of big interest to the farmer in open field in general, and in greenhouses more particularly.
Author Response File: 
Author Response.pdf
Reviewer 2 Report
This is a good review article highlights the deleterious effect of reiterate application of antibiotics in gut and fumigations in soil. The literature review is rich and relevant. The paper’s title match its content. The issue presented in the paper have practical applications. The research topic presented clearly, aim of article clearly specified and realized. The article have a logical layout. The language of article correct. The paper’s conclusions follow logically from the development of the argument. The text adequately illustrated.
Author Response
Reviewer #2
This is a good review article highlights the deleterious effect of reiterate application of antibiotics in gut and fumigations in soil. The literature review is rich and relevant. The paper’s title match its content. The issue presented in the paper have practical applications. The research topic presented clearly, aim of article clearly specified and realized. The article have a logical layout. The language of article correct. The paper’s conclusions follow logically from the development of the argument. The text adequately illustrated.
The authors would like to show their gratitude for the overall positive comment.
Author Response File: Author Response.pdf
Reviewer 3 Report
Even though the topic is interesting and there is a lot of interesting information, this paper reads like an extended literature review without a methodological strategy nor a results section.
If this a review paper, then it needs to clearly stated in the beginning. Otherwise you need to enhance this with a strong results and new knowledge section and some methodological steps.
Please see attachment for detailed comments.
Comments for author File: Comments.pdf
Author Response
Reviewer #3
Even though the topic is interesting and there is a lot of interesting information, this paper reads like an extended literature review without a methodological strategy nor a results section.
If this a review paper, then it needs to clearly stated in the beginning. Otherwise, you need to enhance this with strong results, new knowledge section, and some methodological steps.
Done. The referee is right: this is a concept review paper so miss the methodological and results sections. In detail, the Associated Editor of the Special Issue titled “Soil Quality and Ecosystem Services: Towards a New Perspective of Soil Use and Management” explicitly request this type of paper to us in light of our expertise on this subject area. However, to address the point raised by the referee, in the revised version we highlight the fact that this is a review paper by mentioning in the Abstract and at the end of the Introduction as follows:
1 – Abstract. “Here, we provide an overview of pathogens regulation in soil and mammals gut, highlighting the differences and the similarities between the two systems. First, we provide a review of the ecological mechanisms underlying the regulation of soil and pathogens, as well as the link be-tween disease suppression and soil health”
2 – Introduction. “In this review, we explore the opportunity provided by recent advances of chemical and metagenomical tools in the studies that link organic carbon sources with both microbiota composition and functions to pathogen spread and invasion in soil and animal gut”.
Point 1: Abstract: Well written abstract, I would perhaps wanted 1-2 lines to link it with the importance of sustainability, as this is the journal it is being submitted for. Are there any environmental benefits of this work?
Done. Ok, we changed the last sentence of the Abstract to better clarify the link between microbiota and agro-ecosystem sustainability: “We conclude by discussing general strategies to promote soil microbiota biodiversity, the connection with plant yield and health, and their possible integration through a “One Health” framework”.
Point 2: Introduction: Interesting and well written introduction. Part of it (lines 53-86) reads a lot like a literature review. So perhaps you can consider making this shorter or moving part of it in the literature section.
Please, see response to the first comment of this referee.
Point 3: Line 37: What are you setting as ‘optimal environmental conditions’?
Done. You are right, the sentence was too generic and unclear. The text has been corrected as follows: “Intensive cultivation systems based on monocolture are not resistant to biological invasion of pests and pathogens that can rapidly spread and cause substantial losses to crop production”.
Point 4: Antibiotics, fumigations. Microbiota disruption and disease reappraisal: There is a lot of background information in this section. It is understandable and well written. I would just suggest linking it a bit more with the focus of this study, so it does not read independent. Why are all these relevant to the aims of this paper?
The connection with the general aim of the paper is already clarified at the end of the section as follows: “This section highlights that the application of broad-spectrum biocides on species rich, complex microbiota, like that harbored by mammal’s guts and soils, causes short-term negative effects as well as long-lasting legacy impacts (Figure 1). In both guts and soils, antibiotics and fumigation perturb microbiota equilibrium, enhancing the sus-ceptibility to pathogen reestablishment. Accordingly, with the fluctuating resources hypothesis [44], ecosystems subject to periodical disturbance become prone to biological invasion because their capability to efficiently utilize available resources is drastically reduced. In this regard, the use of aggregate microbiota traits like microbial biomass, total cultivable bacteria, species richness and diversity are all unable to predict the long-lasting negative impact of biocides. Further studies that identify synthetic microbiota traits able to capture the short- and long-term impact of biocide treatments are urgently needed”.
Point 5: Line 201: ‘specie’?
Done. The text has been corrected as follows: “This section highlights that the application of broad-spectrum biocides on species rich, complex microbiota, …”
Point 6: Microbiome stirring to enhance disease suppression: Again, a well written section that reads like an extended literature review. Is this still background? What are the links with the current research? Is this paper only communicates existing findings?
Please, see response to the first comment of this referee.
Point 7: 4. Microbiome transplant: potentiality and drawbacks: A third literature review section. Line 419-420: ‘We compare studies’. Where is the comparison? What are the results? There is no evidence, just literature.
Please, see response to the first comment of this referee.
Point 8: Conclusions & future directions: You mention this is review. If this is just a review of current and past research, you must state it in the abstract and introduction. Up to this point, the reviewer was looking for a methods and results sections. The conclusions text contains interesting facts, but there is no relation to results. The authors have used literature across all paper. If there is a specific methodology focused on literature review, then it needs to be explained. In addition, a results section based on your research and analysis needs to be added.
Please, see response to the first comment of this referee.
Author Response File: Author Response.pdf
Round 2
Reviewer 3 Report
Thank you for the clarifications and review comments. Since it was clarifyied that this is a review paper and not a new knowledge paper, I am fine with the structure and context and indeed there were only minor changes required.
I have no further comments
