The Taxonomic Composition Changes of Bacteria and Fungi in Plant Residue Composts Induced by Biochar and Calcium Carbonate Application
and Tatiana Aksenova 2Round 1
Reviewer 1 Report (Previous Reviewer 4)
The authors summarized and discussed the effect of biochar and calcium carbonate on the bacterial and fungal community’s composition and structure in composts made of different plant residues. This work provides new insight and opinion into the development of organic waste composting as an efficient fertilizer. The manuscript is well-organized and clearly stated.
specific comments:
1. The quality of figures and tables should be improved.
2. Some lasted work should be cited.
Such as：
https://www.sciencedirect.com/science/article/pii/S1385894723001110
https://www.sciencedirect.com/science/article/pii/S2213343723006796
Author Response
Response to Reviewer 1.
Dear reviewer!
We express our deep appreciation for analysis of our manuscript, for your recommendations and for giving us the opportunity to improve the version of our manuscript.
We have tried to take into account your comments and made corrections to the text.
Sincerely yours,
Nataliya Orlova
Dr. Science
Dept. of Agriculture, Faculty of Biology, Saint-Petersburg State University, 199178, 16 line V.O., 29, Saint-Petersburg, Russia, [email protected], tel. +79219281664
Corresponding author
Author Response File: 
Author Response.doc
Reviewer 2 Report (Previous Reviewer 3)
The manuscript describes the taxonomic composition changes of bacteria and fungi in plant residue composts induced by biochar and calcium carbonate application.
The text is generally well-written. Minor language issues exist. All responses must be included in the text. Some points are raised below.
1. Ls. 84-5: More details regarding the biochar production are needed.
2. L.162-3: A description on how does the C:N ratio affected the temp of the compostable material decomposition and the maturation of the compost in the present study is needed.
3. A short explanation describing the effect of CaCO3 and biochar in the composting process is needed.
4. Ls. 170-1: Please, explain.
5. Ls. 241-3: not clear, needs language revision.
6. Ls.244-5: an explanation is needed to support the experimental outcomes.
7. Ls. 285-6: an explanation is also needed to support the experimental outcomes.
8. Ls.299-300: the same.
9. Ls.337-8: Why do you think this happens?
10. L.353: “…if they used in fresh form.” What are the other forms? What happens then?
11. Renumbering of Figures is needed.
Minor editing of English language required
Author Response
Response to Reviewer 2.
Dear reviewer!
Thank you very much for your work with our manuscript, for your recommendations for correcting the text and for giving us the opportunity to improve the version of the submitted manuscript.
We fully agree with the general and specific remarks and according your recommendations inserted changes in the text.
The text of the manuscript has been finalized and corrected.
We tried to explain obtained results and inserted clarifications into the text.
We added information about the quality of biochar, described the influence of the C/N ratio on the composting process.
We tried to explain obtained results and inserted clarifications into the text.
We corrected the numbering of the figures.
And we tried to revise the language.
Thank you very much for work with our manuscript and for given us an opportunity to improve the version of previously submitted manuscript.
Sincerely,
Nataliya Orlova
Dr. Science
Dept. of Agriculture, Faculty of Biology, Saint-Petersburg State University,
199178, 16 line V.O., 29, Saint-Petersburg, Russia,
tel. +79219281664
Corresponding author
Author Response File: Author Response.doc
Reviewer 3 Report (New Reviewer)
The manuscript Agronomy-2609571 “The taxonomic composition changes of bacteria and fungi in plant residue composts induced by biochar and calcium carbonate application” is an adequate article with some interesting and promising results. The investigation reported variations on taxonomic composition of different composting mixtures treated with additives or ameliorants. In general, the manuscript provides an interesting microbiological characterization of composting process, however, it needs some format and English edition.
In this sense, figures and tables should use the same format and provide a proper description of treatments among other antecedents. In terms of development of the article, authors need to improve the introduction and the methodology sections including proper and current references of the conducted analyzes. Moreover, it is critical to respond to the aim of this research, therefore, the article need to include other statistical analyzes that provide evidence about the effect of the additives during the process of composting. I suggest analyzing the relationship of the different variables and include some extra multivariate analyzes to reduce the data.
In my opinion, the article is based on a descriptive analysis and need to enhance presentation and discussion of results.
Therefore, I suggest handling back the manuscript to the authors with major revisions. Some general comments as follow:
Introduction:
- Need a solid justification of the study, which the main difference in comparison to other studies.
Methods:
- The authors need to provide proper references for the proposed analyzes.
- Improve the statistical methods by including other analyzes that enrich the article.
Discussion.
- The description of results is complete but there is a brief discussion of data that need to be improved.
Despite I am not highly qualified english speaker, there are several paragraph that need an extensive editing.
Author Response
Response to Reviewer 3.
Dear reviewer!
We express our deep appreciation for analysis of our manuscript, for your recommendations and comments.
We agree with the general remarks and tried to take them into account and correct our text.
We have finalized the introductory and methodological sections, included relevant links of 2023.
We have added statistical analyses to the work, which confirm the effect of the studied reagents on the microbiota.
We tried to explain obtained results and inserted clarifications into the text.
And we tried to revise the language.
The text of the manuscript has been finalized and corrected.
Sincerely,
Nataliya Orlova
Dr. Science
Dept. of Agriculture, Faculty of Biology, Saint-Petersburg State University,
199178, 16 line V.O., 29, Saint-Petersburg, Russia,
tel. +79219281664
Corresponding author
Author Response File: Author Response.doc
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
The topic and the experimental approach are interesting and timely, and the methods used are largely sound. My main reservations regard the Materials and methods description, some lacking information on the composting process, the lack of analytical data for the mature compost, and one rather crucial element of the experimental design.
The composting part of the experiment is scarcely described, and do not allow for any replication or even overarching understanding of how the composting process ran: There is no description of the size of the composting batches, if these were manipulated during the composting (for mixing, aeration), how aeration was assured and made comparable between treatments, which temperatures were achieved, maintenance of water content, possible losses as liquids or gases, etc. Materials and methods also lack descriptions of some extractions (humic acids) and analyses (total C and N).
The amendments resulted in a significant change in pH in the mature compost, and pH is known to be a major determinant for microbial selection and subsequent proliferation of both fungi and bacteria. It is a major weakness of the study (i.e. the experimental design) that biochar and carbonate inputs were not matched to ensure similar pH in the final composts (or during the composting process; which was unfortunately not assessed). Rather than a comparison of composts with and without biochar, corrected for biochar-induced pH changes, the results of the experiment is now merely a comparison of three random treatments with different pH, which is far less interesting and inconclusive regarding mechanistic explanations. The finding that composts which differ in pH have different microbial communities is to be expected.
The Results do not include any thorough presentation of the resulting composts that could have given clues to why they were different, and what caused these differences. I particularly miss analyses of ash content, and plant available nutrient ions.
The authors also fail to evaluate to which extent the biochar within the mature composts affect the measured parameters (how much does biochar N contribute to compost N? N in biochar is known to have very low bioavailability, and do not contribute to meaningful C/N-rations).
Also, I find it worth mentioning that the “humus” fractionation and its use as a qualitative assessment of organic matter is rather out-dated and should be avoided. It is well known that the fractions resulting from such extractions are artificial (artifacts of the extraction) and non-representative of the forms of organic matter found in soil organic matter. See e.g. Schmidt et al. 2011 (10.1038/nature10386).
Though the microbiology work within this study is solid (sampling, analyses, bioinformatics, statistics), I find these efforts somewhat wasted on an experiment with a poor design, preventing mechanistic explanations and sound conclusions. I this cannot recommend publication of this manuscript.
There are som minor language issues, but these could (heve been) resolved during review.
Reviewer 2 Report
Dear authors and editors,
This paper is poorly written in English and must be thoroughly revised (see comments in the PDF file). This distracts from the scientific value and raises doubts. A PCR-based metagenome method has been employed to describe changes in alpha diversity in different composts that received biochar or calcium carbonate treatments. Treatments were applied to investigate how they would impact composting, influence C:N ratios, and impact on the microbial community. I think too much emphasis was placed on the Phylum level analyses for the bacteria and more should have been given to genus level changes. We would expect calcium carbonate to impact pH and if so, to have an impact on the bacterial community. I don't think the data was studied in enough depth to conclude that there wasn't a change. The fungal diversity did seem to change as a response to the treatments. The data deserve a better-written paper. I recommend the authors resubmit after further bacterial analyses and be much more careful with their English revision. I made some changes to the English in the manuscript.
Comments for author File: 
Comments.pdf
Dear authors and editors,
This paper is poorly written in English and must be thoroughly revised (see comments in the PDF file). This distracts from the scientific value and raises doubts. A PCR-based metagenome method has been employed to describe changes in alpha diversity in different composts that received biochar or calcium carbonate treatments. Treatments were applied to investigate how they would impact composting, influence C:N ratios, and impact on the microbial community. I think too much emphasis was placed on the Phylum level analyses for the bacteria and more should have been given to genus level changes. We would expect calcium carbonate to impact pH and if so, to have an impact on the bacterial community. I don't think the data was studied in enough depth to conclude that there wasn't a change. The fungal diversity did seem to change as a response to the treatments. The data deserve a better-written paper. I recommend the authors resubmit after further bacterial analyses and be much more careful with their English revision. I made some changes to the English in the manuscript.
Reviewer 3 Report
The manuscript describes the taxonomic composition changes of bacteria and fungi in plant residue composts induced by biochar and calcium carbonate application.
The text is generally well-written. Minor language issues exist. Some points are raised below.
1. L. 54: “Such composts are recommended for use as an organic ….”. Please, correct.
2. L.143-4: How does the C:N ratio affect the temp of the compostable material decomposition and the maturation of the compost in the present study?
3. Table 2: pH instead of pHH2O’
4. L.153: “Composting plant residues with biochar resulted in increased pH values and humic acid content in the compost…”. I think this is valid for CaCO3, see Table 1.
5. Ls.178-84: An explanation Is needed for all the experimental data described in these lines.
6. Ls. 216-7: not clear, needs language revision.
7. Ls.218-9: an explanation is needed to support the experimental outcomes.
8. Ls. 282-3: an explanation is also needed to support the experimental outcomes.
9. Ls.297-9: the same.
10. Ls.335-6: Why do you think this happens?
11. L.351: “…if they used in fresh form.” What are the other forms? What happens then?
12. Ls. 357-8: not very clear, language revision required.
The language is generally fluent; minor issues are raised.
Reviewer 4 Report
The authors summarized and discussed the effect of biochar and calcium carbonate on the bacterial and fungal community’s composition and structure in composts made of different plant residues. On this basis, they further investigated the chemical characteristics of composting with different plant residues, number of bacteria and fungi during composting process, performing Phil level analysis and genus level analysis on dominant and common bacteria, division and class level analysis and genus species level analysis of fungal communities. This work provides new insight and opinion into the development of organic waste composting as an efficient fertilizer. The manuscript is well-organized and clearly stated.
The following concerns are addressed for improvement of manuscript.
1.Highlight the innovative points and key points of the article.
2.Oat and rye are used as composting materials, with similar varieties. It is recommended to modify or add other species of plants as experimental materials.
3.The conclusion that rye composting reduced the number of fungi does not match the results shown in Figure 1.
4.The abstract could be more concise.
5.The genus level analysis of bacteria and fungi during the composting process can be simplified.
6.The symbol "℃" in line 80 and line 85 is not consistent.
7. There is an issue with the spacing between lines in line 133.
8. Inconsistent alignment of figure names.
9. There is an issue with the formatting of Table 3.
10. The bold font of "Table 4" in line 352 is inconsistent with the format of other table names.
11. There is a problem with Punctuation in line 366.
12. The alignment of the full text charts is not uniform.
13. The use of Punctuation on lines 329 and 340 is inconsistent.
