Genome description of a potentially novel species of Brevibacterium sp. strain IMA_C3 isolated from an integrated mangrove aquaculture pond
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Brevibacterium sp. strain IMA_C3, a Gram-positive bacterium, was isolated from an integrated mangrove aquaculture pond in close proximity to Sundarbans mangrove. The bacterium was isolated from mangrove leaf litter and grown on Luria-Bertani medium with salinity of 20. The 16S rRNA sequence of this isolateshowed 99.67% identity with Brevibacterium linens AE038-8 from the INSDC DNA databases (GenBank/DDBJ/ENA). Whole-genome sequencing was carried out using long-read sequencing using Oxford Nanopore Technologies chemistry in MinION platform, followed by genome annotation undertaken against the RefSeq and GTDB databases. The genome is approximately 4.1 Mb in size, with G+C content of 64.59%. Functional analysis of the draft genome revealed presence of genes related to complex carbon utilization, nitrogen and phosphate metabolism, and metal transport. Additionally, the genome encodes for secondary metabolites, including ε-Poly-L-lysine, ectoine, terpene, and phenazine, that could have potential applications in controlling viral infections in indigenous shrimp populations within integrated mangrove aquaculture systems.
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Dear Dr Bhadury, Thank you for your submission. Following reviews i have selected major revision. Taking specific note of Reviewer 2's comments, while some are subjective suggestions for improvements there are comments with merit as methodological rigor. Please address their concerns where possible. While novelty is not an essential criteria fro ACMI, i would note that in cases where there has potentially been an over reach in the conclusions drawn (or at least from the in text content), stating clearly limitations of the analysis/data is an acceptable compromise. Also, in regards to species identification, reviewer 2's comments in either using a larger number of Brevibacterium species or rationalising why these were used specifically would be valuable. Please do not hesitate to be in contact with any questions. Best wishes, John
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Comments to Author
The manuscript describes the genome of a Brevibacterium sp. strain IMA_C3 isolated from a mangrove aquaculture pond and presents extensive genomic analyses including assembly, annotation, phylogeny, and predictions on functional gene clusters. While the study has potential and contains a wealth of technical data, there remain significant concerns regarding clarity, experimental rationale, and contextual interpretation that require major revisions before the work could be considered for publication. * The overall novelty of the study is not convincingly demonstrated. Although the 16S rRNA analysis shows high identity (around 99%) with known Brevibacterium strains, the manuscript does not clearly justify the claim of "potentially novel species." The criteria for species delineation need to be more …
Comments to Author
The manuscript describes the genome of a Brevibacterium sp. strain IMA_C3 isolated from a mangrove aquaculture pond and presents extensive genomic analyses including assembly, annotation, phylogeny, and predictions on functional gene clusters. While the study has potential and contains a wealth of technical data, there remain significant concerns regarding clarity, experimental rationale, and contextual interpretation that require major revisions before the work could be considered for publication. * The overall novelty of the study is not convincingly demonstrated. Although the 16S rRNA analysis shows high identity (around 99%) with known Brevibacterium strains, the manuscript does not clearly justify the claim of "potentially novel species." The criteria for species delineation need to be more rigorously discussed using genomic metrics (e.g. ANI thresholds, digital DDH) and compared against a broader dataset. * The rationale behind isolating the bacterium from an integrated mangrove aquaculture pond and linking its genomic features to potential applications (e.g. control of white spot syndrome virus) is speculative. There is insufficient experimental evidence or validation to support the claim that the biosynthetic potential (e.g. ε-Poly-L-lysine, ectoine, terpene, phenazine clusters) translates into bio-control activity. * The methods section, although detailed in many aspects, suffers from lack of clarity in several points. For instance, the description "grown on Luria-Bertani medium of salinity 20" is ambiguous—details of the salinity conditions (e.g. units, rationale for use) need to be explicitly provided. Similarly, the isolation protocol would benefit from clearer justification of each step and discussion of controls or replicates. * In the phylogenetic analysis, while the authors have used standard tools, the dataset seems limited. The manuscript would be strengthened by incorporating a more comprehensive phylogenetic comparison with a larger number of closely related Brevibacterium species. Moreover, the interpretation of the evolutionary relationships and the robustness of the tree topology are not fully discussed. * The analysis of secondary metabolite biosynthetic gene clusters is only superficially addressed. There is a need for a deeper discussion on the predicted products, their novelty, and how they might function in the ecological niche. Experimental or in silico validation of these predictions (e.g. comparison with known clusters) would enhance the impact of the study. * There are several language issues and inconsistencies in the manuscript. Numerous grammatical errors, awkward phrasing (e.g. in the abstract and methods sections), and occasional typographical mistakes reduce the clarity of the presentation. The authors should seek thorough language editing to improve readability. * The manuscript's structure could be improved. For instance, while the methods are exhaustive, there is no dedicated conclusion section to succinctly summarize the findings, implications, and future directions. Additionally, the reference formatting shows inconsistencies that need to be standardized according to the journal's guidelines. * The figures and tables are informative but lack adequate description in the text. The legends and in-text references should be expanded to explain the significance of the data presented, and higher resolution images may be required for clear visualization. * Minor technical details, such as the reporting of genome statistics and assembly metrics, while acceptable, would benefit from a brief discussion on quality control benchmarks (e.g. comparison with standards from Bowers et al.) to contextualize the completeness and quality of the assembly.
Please rate the manuscript for methodological rigour
Satisfactory
Please rate the quality of the presentation and structure of the manuscript
Poor
To what extent are the conclusions supported by the data?
Partially support
Do you have any concerns of possible image manipulation, plagiarism or any other unethical practices?
No
Is there a potential financial or other conflict of interest between yourself and the author(s)?
No
If this manuscript involves human and/or animal work, have the subjects been treated in an ethical manner and the authors complied with the appropriate guidelines?
No: Not applicable
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Comments to Author
The study conducted by Yash et al. entitled Genome description of a potentially novel species of Brevibacterium sp. strain IMA_C3 isolated from an integrated mangrove aquaculture pond describes isolation and sequencing of a new species of Brevibacterium genus. I have few queries regarding manuscript therefore, I suggest following revision: Specific points: 1. Grammatical correction is required in line no 63-65. 2. The hypothesis for conducting the isolation and sequencing study is missing and should be added at the end of introduction section. 3. As mentioned in line no 79 the washed leaf extract was used as inoculum and in LB plates numerous colonies could be observed but on which basis this particular isolate/strain has been selected for going in depth sequencing study and the others were …
Comments to Author
The study conducted by Yash et al. entitled Genome description of a potentially novel species of Brevibacterium sp. strain IMA_C3 isolated from an integrated mangrove aquaculture pond describes isolation and sequencing of a new species of Brevibacterium genus. I have few queries regarding manuscript therefore, I suggest following revision: Specific points: 1. Grammatical correction is required in line no 63-65. 2. The hypothesis for conducting the isolation and sequencing study is missing and should be added at the end of introduction section. 3. As mentioned in line no 79 the washed leaf extract was used as inoculum and in LB plates numerous colonies could be observed but on which basis this particular isolate/strain has been selected for going in depth sequencing study and the others were overlooked is not mentioned in the manuscript. Justification for using this isolate should be incorporated. 4. How this isolate could be useful against white spot syndrome virus (WSSV) shrimps should be addressed more precisely.
Please rate the manuscript for methodological rigour
Satisfactory
Please rate the quality of the presentation and structure of the manuscript
Satisfactory
To what extent are the conclusions supported by the data?
Strongly support
Do you have any concerns of possible image manipulation, plagiarism or any other unethical practices?
No
Is there a potential financial or other conflict of interest between yourself and the author(s)?
No
If this manuscript involves human and/or animal work, have the subjects been treated in an ethical manner and the authors complied with the appropriate guidelines?
Yes
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