Massilia paldalensis sp. nov., Isolated from Stream Bank Soil
Round 1
Reviewer 1 Report
Comments and Suggestions for AuthorsGeneral comments
The authors isolated Massilia sp. TN1-12T from stream bank soil in Korea, sequenced the 16S rRNA and genome, and examined various characteristics. Based on a comparison of the sequences and their characteristics with that of several known Massilia species, the authors proposed that TN1-12T as a new species.
Although the authors properly performed the sequence analysis and characterization (TN1-12T appears to be a new species of Massilia sp.), the manuscript must be considered incomplete as a scientific paper, mainly because of the following points.
Major comments
1. The main content of this manuscript (proposal of TN1-12T as a new species) is not appropriate for this journal “Diversity”. (Regarding this point, I will follow the editor’s decision.) However, to be published in this journal, it is necessary to explain this study and discuss the results from the perspective of “Diversity”.
2. The purpose and significance of this study are not clearly stated in the Introduction. Therefore, the importance and value of the contents of this manuscript are not clear.
3. In this manuscript, only a description of the results is provided, and there is no discussion.
The findings of this study and their relevance to previous findings are not described.
4. Characteristics of TN1-12T and Massilia spp. are shown in the tables, but there is no description or comparison of them.
5. The rationale for selecting TN1-12T needs to be stated. The authors stated “During the investigation of the diversity of the microbiome soil,” in “2.1. Isolation and cultivation”, but only TN1-12T was investigated in this study, which does not correspond to the objective.
Author Response
General comments
The authors isolated Massilia sp. TN1-12T from stream bank soil in Korea, sequenced the 16S rRNA and genome, and examined various characteristics. Based on a comparison of the sequences and their characteristics with that of several known Massilia species, the authors proposed that TN1-12T as a new species.
Although the authors properly performed the sequence analysis and characterization (TN1-12T appears to be a new species of Massilia sp.), the manuscript must be considered incomplete as a scientific paper, mainly because of the following points.
Major comments
- The main content of this manuscript (proposal of TN1-12T as a new species) is not appropriate for this journal “Diversity”. (Regarding this point, I will follow the editor’s decision.) However, to be published in this journal, it is necessary to explain this study and discuss the results from the perspective of “Diversity”.
Answer: Thank you very much for taking the time to review this manuscript. The detailed revisions are outlined in the answer 2 and 3.
- The purpose and significance of this study are not clearly stated in the Introduction. Therefore, the importance and value of the contents of this manuscript are not clear.
Answer: Thank you for pointing this out. We have revised the related sentence (see L38-46)
- In this manuscript, only a description of the results is provided, and there is no discussion. The findings of this study and their relevance to previous findings are not described.
Answer: Thank you for the comments. The discussion has been revised (see L209-222)
- Characteristics of TN1-12T and Massilia spp. are shown in the tables, but there is no description or comparison of them.
Answer: Thank you for the comments. The Physiology and chemotaxonomy has been revised (see L167-179)
- The rationale for selecting TN1-12T needs to be stated. The authors stated “During the investigation of the diversity of the microbiome soil,” in “2.1. Isolation and cultivation”, but only TN1-12T was investigated in this study, which does not correspond to the objective.
Answer: Thank you for your valuable comment. The related sentence has been revised (see L49-50)
Reviewer 2 Report
Comments and Suggestions for AuthorsThe manuscript presents the discovery of Massilia paldalensis sp. nov., a novel bacterial species isolated from stream bank soil. The study provides a comprehensive taxonomic characterization, including phylogenetic analysis, genome annotation, and biochemical profiling. Strengths include thorough genomic comparisons and detailed chemotaxonomic data. However, some issues require attention before publicaiton.
- Clarify the specific criteria for defining Massilia paldalensis as a novel species beyond ANI and dDDH values.
- Improve the introduction by linking Massilia paldalensis to broader ecological or industrial significance.
- Expand the discussion on heavy metal resistance, linking it to previous studies for better context.
- Provide a clearer justification for selecting reference strains in the comparative study
- Specify the coverage depth for whole-genome sequencing to confirm sequencing adequacy.
- Verify that all in-text citations have corresponding references in the reference list.
Author Response
The manuscript presents the discovery of Massilia paldalensis sp. nov., a novel bacterial species isolated from stream bank soil. The study provides a comprehensive taxonomic characterization, including phylogenetic analysis, genome annotation, and biochemical profiling. Strengths include thorough genomic comparisons and detailed chemotaxonomic data. However, some issues require attention before publicaiton.
- Clarify the specific criteria for defining Massilia paldalensis as a novel species beyond ANI and dDDH values.
Answer: Thank you for pointing this out. We have revised in the Discussion (see L209-215)
- Improve the introduction by linking Massilia paldalensis to broader ecological or industrial significance.
Answer: Thanks for highlighting this. The Introduction has been revised (see L38-46)
- Expand the discussion on heavy metal resistance, linking it to previous studies for better context.
Answer: Thank you for the comments. The Discussion has been revised (see L216-222)
- Provide a clearer justification for selecting reference strains in the comparative study
Answer: Thank you for your valuable comment. The related sentence has been revised (see L57-60)
- Specify the coverage depth for whole-genome sequencing to confirm sequencing adequacy.
Answer: Thank you for your valuable comment. The related sentence has been revised (L 137-139)
- Verify that all in-text citations have corresponding references in the reference list.
Answer: Thank you for bringing this to my attention. We have already reviewed the relevant references listed in the reference list.
Reviewer 3 Report
Comments and Suggestions for AuthorsMajor comments
Please provide the accession number where the genome of the type strain is deposited. It is important that the genome is available and listed in the Data Availability Statement. Currently, the Data Availability Statement mentions the following: “No new data was created or analyzed in this study. Data sharing is not applicable to this article”.
In the methods it is necessary to indicate how the genome was assembled. For example, how the reads were processed for quality, what type of filters were used, what parameters were used for assembly using SPAdes.
Minor comments:
In the Abstract, please correct the following: (1) Base(d) on; (2) genus Massilia(italics)
Please correct the following subtitles: (1) 2.2.16. S rRNA gene; (2) 3.1.16. S rRNA gene
Please correct this phrase: “… and assembled by de novo SPAdes (V3.2)27”. Assembled de novo by using SPAdes edited version?
The 16S rRNA contig (¿gene?) had 1,477 bp. Please indicate if the gene sequence is complete. I suggest to replace contig by gene sequence.
Please correct the species name to minors: “observed in the species M. Tieshanensis KACC 14940”
Author Response
Major comments
- Please provide the accession number where the genome of the type strain is deposited. It is important that the genome is available and listed in the Data Availability Statement. Currently, the Data Availability Statement mentions the following: “No new data was created or analyzed in this study. Data sharing is not applicable to this article”.
Answer: Thank you for pointing this out. We have already reviewed and added the accession number in Data Availability Statement (See L275-279)
- In the methods it is necessary to indicate how the genome was assembled. For example, how the reads were processed for quality, what type of filters were used, what parameters were used for assembly using SPAdes.
Answer: Thank you for your valuable comment. The Methods 2.2 and results 3.1 have been revised (see L74-78, 135-139)
Minor comments:
In the Abstract, please correct the following: (1) Base(d) on; (2) genus Massilia(italics)
Answer: revised as suggested (see L10,19)
Please correct the following subtitles: (1) 2.2.16. S rRNA gene; (2) 3.1.16. S rRNA gene
Answer: revised as suggested (see L61,124)
Please correct this phrase: “… and assembled by de novo SPAdes (V3.2)27”. Assembled de novo by using SPAdes edited version?
Answer: revised as suggested (see L76-77)
The 16S rRNA contig (¿gene?) had 1,477 bp. Please indicate if the gene sequence is complete. I suggest to replace contig by gene sequence.
Answer: replaced as suggested (see L125)
Please correct the species name to minors: “observed in the species M. Tieshanensis KACC 14940”
Answer: revised as suggested (see L170)
We have changed sentences based on your valuable comments. Thank you for highlighting these.
Round 2
Reviewer 1 Report
Comments and Suggestions for AuthorsGeneral comment
The authors have responded to my last comments and revised the manuscript, but I feel that most of the responses are not substantive. This study is mainly a report on the description of a new species, and it does not consider diversity, so I think it should be submitted to a journal that is more suitable for that.
Major comments
My last comment 1:
The main content of this manuscript (proposal of TN1-12T as a new species) is not appropriate for this journal “Diversity”. (Regarding this point, I will follow the editor’s decision.) However, to be published in this journal, it is necessary to explain this study and discuss the results from the perspective of “Diversity”.
Answer: Thank you very much for taking the time to review this manuscript. The detailed revisions are outlined in the answer 2 and 3.
My last comment 2: The purpose and significance of this study are not clearly stated in the Introduction. Therefore, the importance and value of the contents of this manuscript are not clear.
Answer: Thank you for pointing this out. We have revised the related sentence (see L38-46)
As only one strain was examined in this study, and no comprehensive discussion of the characteristics was conducted, it does not constitute a report on the “diversity of the Massilia genus”. The authors state that they have made revisions, but as far as I can tell from reading the revised text, (although there are some parts where it is a comparison with known strains) it does not constitute a discussion of diversity.
The authors stated that the purpose of this study is “This study aims to characterize a novel strain, TN1-12T, belonging to the genus Massilia, which was isolated from stream bank soil in the Paldal district of Suwon City, Korea., (L38-39)”. However, the significance of publishing this study conducted for this purpose in this journal “diversity” is unclear.
Furthermore, the authors stated that “The research seeks to confirm its classification as a new species, contributing to the understanding of soil microbiome diversity and the taxonomic expansion of the genus. (L40-41)”. However, this research only investigated the Massilia genus, and the diversity of soil microorganisms is not discussed. In addition, it is not clear which part of the taxonomic expansion of the genus is being discussed.
In conclusion, if the first objective (L38-39) is the main topic of this manuscript, the authors should submit it in a journal that suits it. On the other hand, if the second objective (L40-43) is the main topic of this manuscript and it is published in this journal, the authors need to completely renew the content to suit the theme of this journal.
My last comment 3: In this manuscript, only a description of the results is provided, and there is no discussion. The findings of this study and their relevance to previous findings are not described.
Answer: Thank you for the comments. The discussion has been revised (see L209-222)
The majority of the revised parts are explanations of the results of the comparison. The final sentence seems to be a discussion, but there is no logical process from the results to the discussion. In addition, there is no explanation of diversity. Furthermore, the majority of the discussion (L223-) is still an explanation of the results. The author needs to explain how they considered the results obtained and what they found in this study, rather than simply listing the results.
My last comment 4: Characteristics of TN1-12T and Massilia spp. are shown in the tables, but there is no description or comparison of them.
Answer: Thank you for the comments. The Physiology and chemotaxonomy has been revised (see L167-179)
The authors need to explain which and how characteristics differ from known strains, and how diverse they are, how far the diversity was expanded in this study. In “Detailed differential characteristics are given in Table 1.” (L178), the reader does not know where to focus their attention or what the authors focused on in their discussion.
My last comment 5: The rationale for selecting TN1-12T needs to be stated. The authors stated “During the investigation of the diversity of the microbiome soil,” in “2.1. Isolation and cultivation”, but only TN1-12T was investigated in this study, which does not correspond to the objective.
Answer: Thank you for your valuable comment. The related sentence has been revised (see L49-50)
As before, the purpose of this study (L40-) does not match the fact that the authors chose only this strain.
Author Response
My last comment 1:
The main content of this manuscript (proposal of TN1-12T as a new species) is not appropriate for this journal “Diversity”. (Regarding this point, I will follow the editor’s decision.) However, to be published in this journal, it is necessary to explain this study and discuss the results from the perspective of “Diversity”.
Answer: Thank you very much for taking the time to review this manuscript. The detailed revisions are outlined in the answer 2 and 3.
My last comment 2: The purpose and significance of this study are not clearly stated in the Introduction. Therefore, the importance and value of the contents of this manuscript are not clear.
Answer: Thank you for pointing this out. We have revised the related sentence (see L38-46)
Reply: revised as suggested (see L38-45)
As only one strain was examined in this study, and no comprehensive discussion of the characteristics was conducted, it does not constitute a report on the “diversity of the Massilia genus”. The authors state that they have made revisions, but as far as I can tell from reading the revised text, (although there are some parts where it is a comparison with known strains) it does not constitute a discussion of diversity.
Reply: revised as suggested (see L224-226 & L232-234)
The authors stated that the purpose of this study is “This study aims to characterize a novel strain, TN1-12T, belonging to the genus Massilia, which was isolated from stream bank soil in the Paldal district of Suwon City, Korea., (L38-39)”. However, the significance of publishing this study conducted for this purpose in this journal “diversity” is unclear.
Furthermore, the authors stated that “The research seeks to confirm its classification as a new species, contributing to the understanding of soil microbiome diversity and the taxonomic expansion of the genus. (L40-41)”. However, this research only investigated the Massilia genus, and the diversity of soil microorganisms is not discussed. In addition, it is not clear which part of the taxonomic expansion of the genus is being discussed.
Reply: revised as suggested (see L232-234)
In conclusion, if the first objective (L38-39) is the main topic of this manuscript, the authors should submit it in a journal that suits it. On the other hand, if the second objective (L40-43) is the main topic of this manuscript and it is published in this journal, the authors need to completely renew the content to suit the theme of this journal.
Reply: revised as we could (see L43-49) because this journal includes systematic scope as diversity.
My last comment 3: In this manuscript, only a description of the results is provided, and there is no discussion. The findings of this study and their relevance to previous findings are not described.
Answer: Thank you for the comments. The discussion has been revised (see L209-222)
The majority of the revised parts are explanations of the results of the comparison. The final sentence seems to be a discussion, but there is no logical process from the results to the discussion. In addition, there is no explanation of diversity. Furthermore, the majority of the discussion (L223-) is still an explanation of the results. The author needs to explain how they considered the results obtained and what they found in this study, rather than simply listing the results.
Reply: revised as we could (see L224-250)
My last comment 4: Characteristics of TN1-12T and Massilia spp. are shown in the tables, but there is no description or comparison of them.
Answer: Thank you for the comments. The Physiology and chemotaxonomy has been revised (see L167-179)
The authors need to explain which and how characteristics differ from known strains, and how diverse they are, how far the diversity was expanded in this study. In “Detailed differential characteristics are given in Table 1.” (L178), the reader does not know where to focus their attention or what the authors focused on in their discussion.
Reply: revised as suggested (see L182-187 & L191-196)
My last comment 5: The rationale for selecting TN1-12T needs to be stated. The authors stated “During the investigation of the diversity of the microbiome soil,” in “2.1. Isolation and cultivation”, but only TN1-12T was investigated in this study, which does not correspond to the objective.
Answer: Thank you for your valuable comment. The related sentence has been revised (see L49-50)
As before, the purpose of this study (L40-) does not match the fact that the authors chose only this strain.
Reply: revised as suggested (see L38-42)
Author Response File: 
Author Response.docx
