Addition of Chicken Litter Compost Changes Bacteriobiome in Fallow Soil

Comment #1

The introduction should be supplemented with a paragraph on fallow soils, the need to conduct research on these soils and include them in production.

Response #1

Supplemented, thank you!

Comment #2

Materials and Methods Chapter. In this chapter, the authors included 2 tables that concern the properties of compost and soil properties. If these are the authors' own results, this should be transferred to the research results as a characteristic of soil and compost.

Response #2

Yes, these are our own results, but since they are not the main target of research, being just used as a background information about the soil, we followed the stance of many other researchers, who, in order not to overload the results part, put such information in the M&M section. We also added brief description of the methods used to measure soil properties.

Comment #3

I suggest changing the last subsection to a conclusions or summary chapter.

Response #3

Changed as suggested.

Comment #1

The final paragraph of the abstract should include how the research conclusions contribute to the field, what goals were achieved, and the impacts on the ecosystem.

Response #1

Unfortunately, the abstracts in the MDPI-journals are limited to 200 words, not providing too much room for adding more text. We expended the last sentence of the abstract, by finding room by restructuring a bit some preceding sentences. The goal achieved is clear from the main results, which we did no want to remove from the Abstract as its most important part, substituting with general thoughts about environmental significance, etc. The contribution to the field and the potential impact on ecosystems were addressed in the Conclusions section.

Comment #2

Line14, 26, 62, and 67, standardize the description of the experimental regions mentioned and ensure consistency throughout the text.

Response #2

The line 26 contains “West Siberia” as a keyword. It is a geographical region where the city of Novosibirsk is located. Since with the aim of broaden the net that can help the article to be found by more searches, many journals explicitly recommend to use the keywords that do not repeat the words in the title of the Abstract: in this case standardization may be counterproductive.

Comment #3

The introduction is somewhat brief. Line 57–64, need a more in-depth discussion of existing research findings and gaps, as well as the innovation and importance of this study. Additionally, reorganize the language to present the hypotheses of the experiment.

Response #3

We tried to provide a succinct, yet at the same time concise and brief synthesis of the background information for our research. Recent years have been seeing increasingly talkative introductions (due to AI?), but we believe that too long introductions can often be counterproductive as they a) bore readers, and b) eventually may confuse them about the relevance of the provided info to the aim of the study. More in-depth discussion is provided in the Discussion section.

Comment #4

The Materials and Methods section should be supplemented with additional information about the region's precipitation, sunlight hours, and long-term average temperature.

Response #4

The suggested infomation added.

Comment #5

Line 73 and 91, standardize the coordinates mentioned.

Response #5

Corrected by removing the erroneous coordinates in Line 73 (of the version you reviewed).

Comment #6

Line 94, specify the process for handling soil samples after collection and briefly describe the methods used for testing soil properties.

Response #6

Specified and described as recommended.

Comment #7

The experimental design section lacks details on the size of the experimental plots. Please include this information.

Response #7

The size of the experimental plots indicated.

Comment #8

Tables 1 and 2 should use a three-line table format and be optimized for aesthetic presentation.

Response #8

Unfortunately, we did not understand your comment about the format; as for the aesthetics, tastes differ, and as soon as the tables are not cumbersome, being easy to grasp, we believe them to be aesthetic enough for a research paper, don’t you?

Comment #9

You should describe abbreviations first and then use them. Please read the journal requirements for details.

Response #9

Corrected, thank you.

Comment #10

Line 157, there is an error, please check and correct it.

Response #10

Corrected, thank you.

Comment #11

There are numerous formatting errors in the references, including missing DOIs, incomplete author lists, and punctuation mistakes. Please carefully review the journal requirements and make the necessary corrections.

Response #11

We did as advised, and reduced the number of authors in 3 references, and in 2 references expended to the full list. Unfortunately, we were not able to find even a single formatting error in the references, let alone the numerous ones; also no missing DOIs and punctuation mistakes.

Comment #12

The language and organization of the article have room for further improvement. It is recommended to revise carefully to enhance the logic and readability of the article.

Response #12

Undoubtedly, there is always room for further improvement in everything! However, it often can be counter-productive. As for the readability, you are the first one to comment on it like you did, because over the years many of our reviewers enjoyed and commended specifically on the style and readability (even with this one). Thus the only thing we can say that we are sincerely sorry that you had found out manuscript not easy to read and hence to review!

Comment #1

The title of the paper should be changed because the authors did not study compost but raw substrate from a chicken farm. Therefore, the word "compost" should be removed.

Response #1

We could not possibly understand why you have come to such conclusion? It was compost, and we described what it was (lines 84-86 in the version you reviewed), but now in the revised version added some more information.

Comment #2

The word "compost" should be removed throughout the manuscript because the methodology does not indicate that the authors used compost. The word "compost" should be replaced with "chicken litter" in the Abstract, Results and Discussion.

Response #2

With all due respect, but it was chicken litter compost.

On the surface in the chicken coops and bigger industrial chicken (or other poultry, for that matter) facilities a layer of sawdust or woody shavings or a mixture of both are commonly spread for collecting birds’ droppings; after a while the litter is substituted with a fresh one.

After the chicken litter is removed from the coop/housing, it is piled in the open field in some kind of big storage sites. Diverse microorganisms perform transformation of the organic mass. Aeration is important for proper decomposition, so piles are usually mixed once in a while. A compost pile with the right ratio of carbon to nitrogen and with adequate moisture will produce enough heat during decomposition to kill many pathogens and seeds. When the individual structure of the material changes, becoming more uniform, as well as the color and odor, chemical and physical properties, and the composted mass no longer has increased temperature, the compost is ready for use.

In our case the used litter was removed to the open field, where it underwent aerobic decomposition (not to confuse it with fermentation, which is an anaerobic process to produce the so called fermentate from various organic substances, including manure).

We did not prepare the compost ourselves, but received it ready-for-use from the local industrial chicken-producing facility.

Comment #3

The Introduction chapter is synthetically written.

Response #3

We tried to provide a succinct, but at the same time concise and brief synthesis of the background information for our research. Detailed analysis would be more relevant for a review of the topic, rather than original research article, would it not?

In the revised version we added some info about fallow soils though.

Comment #4

The chapter "Materials and methods" should be expanded. In this chapter it should be written how big the research plots were? The area from which the soil samples were taken and the method used. It is not clear from the description of this subchapter that the effect of compost (CLC) was tested, only unfermented substrate from chicken farming. It is not known whether this substrate was ploughed or left on the soil surface.

Response #5

The relevant information added.

As we indicated above, chicken litter underwent aerial decomposition in the open field, it was never intended to be fermented, as it is an entirely different (anaerobic) technology.

Comment #5

There is also no characterization of soils from the field without CLC and with CLC before the application of CLC. Such a characterization would provide a clear answer as to whether the effect was solely due to the application of CLC or to some extent due to soil variability.

Response #5

We are afraid we did not get your point here, as there were no soil with CLC before the application of CLC. Therefore we could not possibly fathom how it would provide a clearer answer. As for the variability between the study sites, it is perfectly accounted for by ANOVA applied for statistical analysis of the data.

Comment #6

Table 3. Bacteriobiome composition of chicken litter compost (relative abundance, mean ± standard deviation, n=3) after relative abundance should be inserted %.

Response #6

Corrected, thank you.

Comment #7

Arrange Tables 3, 5, 6. Use points in all of them. Also work on the quality of Figure 3, in particular to make the names of the microorganisms more visible.

Response #7

Thank you, the Tables are corrected? And the Figure improved.

Comment #8

Instead of subsection "4.4. General comments" I suggest a chapter "5. Conclusions".

Response #8

Thank you for you recommendation! We did as recommended.

Comment #1

The title of the work is not specific. It is clear that the addition of CLC will change the soil microbiome, but how? In which direction? It would be desirable for this to be reflected in the title already.

Response #1

It might be the case, but we could not come up with something along the suggested lines and reasonably not cumbersome; besides, the intrigue would be lost, would it not? Why bother reading the entire stuff if the main thing is already presented for fast consumption?

Comment #2

How was the manure composted? For how long? Were additional preparations added to accelerate composting (according to the high content of bacilli and low content of pathogens - yes)?

Response #2

The used chicken litter was composted for several months in the open field (described in lines 84-86 of the version you reviewed) without any special additions, but mixed once in a while for better aeration. We added “without any special additions, but mixed once in a while for better aeration” in the revised version.

Comment #3

In Table 1, the sum of components is significantly higher than 100%.

Response #3

Thank you very much for pointing the error! Corrected.

Comment #4

Assessment of compost pathogenicity?

Response #5

We did not check the compost; but chicken litter at the chicken producing facility is regularly checked according to the respective norm and regulations of the country, otherwise the used litter would not be released into an open field.

Comment #5

How did the microbiome of the CLC itself change over time?

Response #5

We do not study the issue, but undoubtedly some changes occur depending on the specific environment, specific use and duration of time.

Comment #6

The work is skillfully designed in terms of conducting, presenting, and analyzing bioinformatic data, but the practical value of the work is not fully understood. In terms of agriculture, to predict crop yield, factors such as the application of both chemical and biological fertilizers, various pesticides, and the microflora introduced with the seed material need to be taken into account.

Response #6

You are absolutely right: any agronomical practice is highly contextual. With this study, though, we did not intend to give any practical advice, except for showing that compost bacterial biomarkers can persist in soil. There is some useful outcome, though:  sometimes researchers happen to claim that the soil under study has never received any manure/manure compost/chicken litter compost, but the presence of “gut” biomarkers can cast doubt on such claims.

Comment #1

The 'Introduction' section provides a good background to the research carried out.

Response #1

Thank you very much!

Comment #2

The "Materials and Methods" section needs improvement. At present, it is not known how the compost was prepared and for how many months. It is also not specified how exactly it was applied to the soil. There is also no information on how the soil samples were taken, the area of the experimental plots, etc. Please give the content of phosphorus and potassium in manure (Table 1) and soil (Table 2) in elemental form, not in oxide form. Please give the content of phosphorus and potassium in manure (Table 1) and soil (Table 2) in elemental form, not in oxide form.

Response #2

The manuscript stated (lines 84-86) that “The CLC represents a litter of wood sawdust, that had been spread on the ground in chicken housing, collecting their droppings; after a while the litter was removed to the open field, where it underwent aerobic decomposition”. We added “, i.e. composting during at least three months at positive temperatures, without any special additions, but mixed once in a while for better aeration.”.

As suggested, we substituted in Tables oxides with respective elements.

Comment #3

My only suggestion - write all the numbers in the tables correctly. Use full stops because it is different now, i.e. sometimes there are full stops and sometimes there are commas (Tables 3, 5, 6). Please improve the quality of Figure 3 because the names of the microorganisms are very hard to see.

Response #3

We corrected the numbers in the indicated Tables, but decided not to do it in red. Ass for the Figure, you must have meant Figure 1. Unfortunately, we produced the graphs in the PAST software, which does not provide many options to improve the graph quality, except or putting in a bigger graph.

Comment #4

Instead of subsection "4.4. General comments", include a chapter 'Conclusions' in which you briefly write the main conclusions from your research. Include the main strengths and weaknesses of your research.

Response #4

We believe the General comments section contains the main conclusions, but describing the main pros and cons of the research in this section does not accords with its genre, being appropriate in Discussion. Besides, although we as a team sometimes described such aspect of our research, now we believe it productive to skip them, as it is obviously the first step of a more detailed study (pending funding).