Genomic insights into indole-3-acetic acid catabolism in the marine algae-associated bacterium, Marinomonas sp. NFXS50
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Auxins, mainly in the form of indole-3-acetic acid (IAA), regulate several aspects of plant and algal growth and development. Consequently, plant and algae-associated bacteria developed the ability to modulate IAA levels, including IAA catabolism. In this work, we present and analyse the genome sequence of the IAA-degrading and marine algae-associated bacterium, Marinomonas sp. NFXS50, analyse its IAA catabolism gene cluster and study the prevalence of IAA catabolism genes in other Marinomonas genomes. Our findings revealed the presence of homologs of the Pseudomonas iac gene cluster, implicated in IAA catabolism, in the genome of strain NFXS50; however, differences were observed in the content and organization of the Marinomonas iac gene cluster when compared to that of the model iac -containing Pseudomonas putida 1290. These variations suggest potential adaptations in the IAA catabolism pathway, possibly influenced by substrate availability and evolutionary factors. The prevalence of iac genes across several Marinomonas species underscores the significance of IAA catabolism in marine environments, potentially influencing plant/algae-bacteria interactions. This study provides novel insights into the IAA catabolism in Marinomonas , laying the groundwork for future investigations into the role of iac genes in Marinomonas physiology and the regulation of marine plant/algae-bacteria interactions.
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The work presented is clear and the arguments well formed. This is a study that would be of interest to the field and community. The reviewers have highlighted major concerns with the work presented. Please ensure that you address their comments.
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The work presented is clear and the arguments well formed. This study would be a valuable contribution to the existing literature. The reviewers have highlighted minor concerns with the work presented. Please ensure that you address their comments. Please provide more detail in the Methods section and ensure that software is consistently cited and its version and parameters included.
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Comments to Author
Manuscript title Genomic insights into indole-3-acetic acid catabolism in the marine algae-associated bacterium, Marinomonas sp. NFXS50 SYNOPSIS AND OVERVIEW Overall, the manuscript is well-written and the study design is also clearly defined. All the results are congruent with the proposed methods to unveil the conservation of IAA catabolism in the Marinonomas genus. The major changes would primarily include building up some concepts in the Introduction, adjusting methods adding some missing information, and improving the plotting and presentation of results, particularly in the phylogeny section. DETAILED REVIEW Abstract Line 36 Specify briefly if this is a model Pseudomonas putida strain for studying IAA metabolism, such as pointed out in the Introduction section. Introduction Lines 64-68 The …
Comments to Author
Manuscript title Genomic insights into indole-3-acetic acid catabolism in the marine algae-associated bacterium, Marinomonas sp. NFXS50 SYNOPSIS AND OVERVIEW Overall, the manuscript is well-written and the study design is also clearly defined. All the results are congruent with the proposed methods to unveil the conservation of IAA catabolism in the Marinonomas genus. The major changes would primarily include building up some concepts in the Introduction, adjusting methods adding some missing information, and improving the plotting and presentation of results, particularly in the phylogeny section. DETAILED REVIEW Abstract Line 36 Specify briefly if this is a model Pseudomonas putida strain for studying IAA metabolism, such as pointed out in the Introduction section. Introduction Lines 64-68 The authors could detail more about the IAA microbial catabolism, genomic organisation of the iac cluster and its occurrence in different microbial taxa. Line 75 Introduce formally the Marinonomas genus (taxonomy, ecology and relevance) before straightforwardly relating their members with IAA catabolism. Methods Line 90 Provide culture conditions (incubation time, temperature). Line 91 Add the localisation of the company's headquarters, such as: "(Sigma-Aldrich, Burlington, MA, United States)". Line 92 Which MiSeq platform? Line 94 Correct, it's SOAPdenovo2. Which release of SOAPdenovo? Line 96 Provide reasoning for the selection of this Marinomonas strain for reference-oriented genome assembly. Line 98 Include the reference for the NCBI guidelines with this particularity regarding the introduction of gap regions during contig joining. Line 99 Which release of the NCBI Prokaryotic Genome Annotation Pipeline? Line 101 Correct "antiSMASH". Line 115 Include the right link for referencing the Marinomonas genomes downloaded from the NCBI GenBank database. Line 117 Why a total of 57 Marinomonas genomes were selected for the comparative genomic analysis? In the GTDB database, there is a total of 91 Marinomonas genomes promptly available. Lines 119-121 The purpose of this phylogenetic inference is not clear… explain how exactly reconstructing the rpoB phylogeny and associating it with the prevalence of iac genes in Marinonomonas. Could it be worthy adding a heatmap or any other visual element showcasing the gene density of the iac genes in Marinomonas? Line 122 Add the MUSCLE version applied for the phylogenetic reconstruction. Results Line 134 Increase the size of both the genomic map and the alignment between the genomic regions in Figure 1. Legends should also be adjusted in that regard. Lines 134-136 Provide more details in the Figure 1 legend, including the accession numbers for both Marinomonas genomes. Line 143 Correct: "antiSMASH". Lines 143-144 antiSMASH results (BGC regions with the highest similarity scores and/or a table summarising the main results) could be provided at this point of the text. Line 165 Italicise "lacH". Lines 170-172 Are both Marinonomonas clusters present in this image? Please, consider re-editing this image. Lines 180-183 Which is the tree outgroup? Don't italicise the strains' ID and include rpoB accession numbers between parentheses. Additionaly, data is missing in the Figure 3 legend, particularly about the phylogeny reconstruction; please rewrite to accommodate a full description of the phylogenetic inference. Strongly suggest replacing the word "phylogram", it is an odd one. Lines 196-197 Add the accession numbers (between parenthesis) for the genome sequences of these cited Marinomonas species for which the gene encoding the alpha-hydroxy acid dehydrogenase family enzyme was not found. Line 225 Replace "N" with "nitrogen".
Please rate the manuscript for methodological rigour
Very good
Please rate the quality of the presentation and structure of the manuscript
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
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Comments to Author
The manuscript is clearly written. Figures follow general standards of genome papers. I just have few points that I would like you to check/address: 1. Line 28: algal instead of algae 2. Line71: strain? Please cross-check. Genera-level differences are seen. But please sure strain is accurate here or not. 3. Since the manuscript focuses on algae from marine environment, maybe dont write plant/algae? Just a suggestion. 4. Line 76: suggest an important role in IAA degradation
Please rate the manuscript for methodological rigour
Good
Please rate the quality of the presentation and structure of the manuscript
Good
To what extent are the conclusions supported by the data?
Strongly support
Do you have any concerns of possible image …
Comments to Author
The manuscript is clearly written. Figures follow general standards of genome papers. I just have few points that I would like you to check/address: 1. Line 28: algal instead of algae 2. Line71: strain? Please cross-check. Genera-level differences are seen. But please sure strain is accurate here or not. 3. Since the manuscript focuses on algae from marine environment, maybe dont write plant/algae? Just a suggestion. 4. Line 76: suggest an important role in IAA degradation
Please rate the manuscript for methodological rigour
Good
Please rate the quality of the presentation and structure of the manuscript
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
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