Delving deep into the draft genome of Mangrovibacter sp. SLW1, isolated from Sundarbans mangrove

  1. Arindam Roy
  2. Anwesha Ghosh
  3. Punyasloke Bhadury

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Abstract

Mangrovibacter sp. SLW1, a Gram-negative, aerobic, motile bacterium, was isolated from mangrove litterfall in Sundarbans mangrove. The draft genome is 5.5 Mbp in size with 49.45 mol% guanine-cytosine (GC) content. The linear chromosome of the bacterium consists of 27 contigs with 7339 coding sequences. The detailed in silico analyses of the genome of Mangrovibacter sp. SLW1 provide information on ecological adaptation. The genome is a reservoir for multiple heavy metals and metalloid resistance gene clusters as well as exhibit metabolic capabilities for utilization of a wide range of carbohydrates. It also encodes for tris-catecholate siderophore and can regulate uptake of iron thereby may influence plant growth such as mangrove vegetation.

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  1. Version published to 10.1099/acmi.0.000847.v3 on Access Microbiology
  3. Version published to 10.1099/acmi.0.000847.v2 on Access Microbiology
  4. Access Microbiology

    Minor comments: Line 51: "from ‘true’ mangrove" What do you mean by true ? Line 65: "Assembled genome quality was evaluated..." Did the authors undertake a genome completeness (e.g. CheckM) assessment? If not, please provide this. Line 77: "in type strain genome server " Please provide more details here. Line 80: "...strain SLW1" ? The authors may want to introduce this strain first and that they decide to name the isolated strain as strain SLW1 because it is not so obvious in the current language. Line 89: What is GGDC? Line 91: "The 16S rRNA based phylogeny" This phylogeny is very limited. Why not undertake a phylogenomic classification? Line 152-153: "facing risk from different types of pollutants". This is confusing. Please rephrase this. Major comments: The abstract details " tris-catecholate siderophore"; however, there is no such results/discussion mention in the main text. Can authors confirm on this? What is unique with strain SLW1? Has authors compared this with other Mangrovibacter species? A comparison with other strain or species may reveal common pathways among Mangrovibacter or adaptation to environmental settings. Table 1 shows the genomic features of SLW1. I recommend authors to include closely related strains/species so as to show the difference in genomic features between SLW1 and other. This can be provided as a supplementary.

  5. Access Microbiology

    Comments to Author

    Abstract Line 22 Correct "gram-negative": "Gram-negative". Line 24 Correct "7339": "7,399". Lines 25-26 Rewrite this sentence for clarity, "ecological information" is particularly confusing. Maybe starting it by stating that through "in-depth in silico analyses, the genome investigation of the Mangrovibacter sp. SLW1 strain revealed ky information on their ecological adaptation". Announcement Line 45 Add a comma after "Enterobacteriaceae". Line 50 Add space between "et al." and "2015". Line 68 Correct "carbohydrate active enzymes": "carbohydrate-active enzymes". Line 70 Write "array" in the plural form: "arrays". Line 71 Correct "post translationally": "post-translationally". Line 73 Replace "antibiotic" with "antimicrobial". Line 77 Capitalize the words for the TYGS: "Type (Strain) Genome Server (TYGS)". Line 79 Add "the" after "DSMZ". Line 80 Add a comma before "respectively". Line 80 Correct "84916": "84,916". Line 81 Correct "325123327": "325,123,327". Line 81 Adjust this genome map image, it is hard to distinguish the presentation of gene features and it is missing GC content, GC skew. Line 82 Why so many contigs were produced using a third-generation sequencing platform? The authors should provide some reasoning for that. Line 83 Correct "835533946": "835,533,946". Line 83 Correct "3259965": "3,259,965". Line 85 Correct "7339": "7,399". Line 86 Correct: "2769": "2,769". Line 91 The phylogenetic tree needs to be urgently revisioned. Italicise genus and species names, write in bold or add some marker for the strain investigated in this survey and add a higher number of Mangrovibacter 16S rRNA gene sequences in this analysis, prioritising the ones from the type strains of the 3 validly accepted species and other isolated from distinct geographic locations. Most importantly, all bootstrap values on the tree should be included. Figure 2 legend also needs to be rewritten since the details on phylogenetic tree reconstruction (evolutionary method for tree estimation, best-fit substitution model, number of bootstraps replicates), particularly highlighting the selected outgroup. Line 96-97 The fact that the strain is catalase positive can't be extrapolated to this environmental stress tolerance capacity, better to rewrite. Line 99 Write in the plural form "glycoside hydrolase". Line 112 Correct "1985": "1,985". Line 116 Write "Bottromycin" in the lowercase: "bottromycin". Line 119 Rephrase these sentences with antiSMASH results. No need to specify the particular regions, just summarise the main classes of BGCs discovered and mention the identity thresholds if you judge necessary. Line 121 Remove the word "synthesis". Line 122 Capitalize "pks": "PKS". Also, which PKS class? Line 123 Remove the word "antibiotic". Additionally, italicize "emrR". Lines 123-124 Italicize "emrR", "rsmA" and "qacG". Line 124 Finish the sentence by adding a dot before "The". Line 135 Italicize "mntH". Line 136 Italicize "arsC". Line 138 Italicize "yadG". Line 140 Italicize "corC". Line 141 Italicize "rcnB". Line 272 Correct the numbers in thousands in Table 1 (add commas).

    Please rate the manuscript for methodological rigour

    Good

    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

  6. Access Microbiology

    Comments to Author

    Please include methodology & discussion part in detail. Please include CRISPR CAS array graphical explanation

    Please rate the manuscript for methodological rigour

    Very good

    Please rate the quality of the presentation and structure of the manuscript

    Very good

    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

  7. Version published to 10.1099/acmi.0.000847.v1 on Access Microbiology