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This is an interesting study, and valuable contribution.
I believe that you will find the recommendations of the reviewers to be straightforward. While I do agree with the second reviewer that this would be a much more valuable contribution if it included some analysis and discussion, there is precedent for PeerJ to accept what is essentially a data report and thus it is left to you to decide to keep this in its current format or expand it.
In their study, Jégousse and co-workers describe 219 archaeal and bacterial MAGs reconstructed from 31 metagenomes taken close to Iceland. The manuscript is well organized and written. It contains most of the information necessary for this type of article (see details below). The figures are appealing. The raw data has been deposited in a public repository.
Te manuscript is a data report. The methods section is fine but the information about the co assembly and the binning is missing (You need to check the figure and the results to llearn which tools were used). In addition, the authors should provide version numbers for all tools used (MegaHIT, CheckM, MetaBAT2, CONCOOT, MaxBin2, prodigal and so on). Also provide the version of the GTDB database.
All data has been provided with one exception. Please upload your MAGs to GenBank (the fasta file for each MAG). Otherwise this important information is not available to researchers.
Good Job. Only my previous comments and three minor comments:
Line 18: ... and sink lower depths of the ocean. -> Rephrase.
Line 23: (please change to) ... to bridge this knowledge gap.
Line 49: uncultured microorganisms (change to) -> yet uncultured marine lineages
All looks good.
The research question - describing a set of MAGs from Icelandic waters - is not relevant or meaningful. This is a nice dataset but there is no real research question in this manuscript, just a description of MAGs. It is too descriptive without posed or addressing an interesting research question. (See comments below.)
Jégousse and colleagues describe a unique metagenomic dataset, including 31 shotgun metagenomes from coastal Icelandic waters and a set of MAGs reconstructed from these samples. They included a mock marine microbial community in these analyses as well. The dataset described here is excellent and fills a needed hole in the databases of marine metagenomic data, but there is not much of a story in the manuscript other than describing the MAGs – it describes the dataset but does not emphasize question/conclusions other than “can we get MAGs from these samples.” This is perhaps best underscored in the first line of the Conclusions section: the goal of just “reconstruct[ing] MAGs from 31 samples from Icelandic sea waters” is not very exciting. I therefore believe there is little scientific merit in the manuscript as currently written. Yes, this is a great dataset (and a very nice MAG collection), but what does it mean? What can it teach us about marine microbiology? As currently written, I believe the manuscript is appropriate for a more descriptive journal (e.g., Microbiology Resource Announcements, Scientific Data) than a journal focused on research findings, but it has a TON of potential, as the metagenomes and MAGs are very nicely done and undoubtedly rich with information.
My suggestion is to use the manuscript as currently written as a starting point to write a longer, more detailed manuscript actually analyzing the MAGs. What are their read mapping patterns across samples? What interesting metabolic genes/pathways are present? Are there any connections between the distribution of MAGs and the unique physical setting of these samples? Etc. There could even be more of an emphasis on comparing the binning algorithms and recovery of the mock community, to make this more of a MAG methodology paper instead of a microbial ecology paper.
However, I will re-emphasize that this is a really nice set of metagenomes and MAGs, and I recognize the amount of hard work that the authors have undergone to get the dataset to this point. In my opinion this work would be put to much better use if the manuscript told an actual story or two instead of just describing the MAG set.
Lines 15-24: Give more detail of any results in the Abstract. It mostly just sets up why the samples are interesting, but I am more interested in what was found. Cut out some of the background on the study site, etc. to make more space if needed.
Lines 95-104: Add information here about quality-control steps (trimming low-quality sequences, etc.) as well as assembly and binning software and parameters. In particular, please make note of any software parameters that deviate from defaults. I realize some of this information is in Fig. 1B but it should also be in this section.
Lines 125-126: A comment – instead of just picking the MetaBat2 MAGs only, the authors could consider using DAS Tool (https://doi.org/10.1038/s41564-018-0171-1, https://github.com/cmks/DAS_Tool) to select a set of non-redundant MAGs from the results of all three binning algorithms. (Which may increase the diversity of MAGs in the final set.) It is nice to see more benchmarking of binning algorithms and mock community work.
Lines 116-182: No analysis of read mapping to MAGs across the metagenomes? Or genes/pathways present in the MAGs? I would really love to see this, in addition to knowing the phylogenetic identity of the MAGs. Without any of these types of analyses I don’t think this article has enough to justify publication as a research article (though as I note above, it could be published as a descriptive article just laying out the dataset).
Lines 174-176: This is confusing. MGIIa-L2 and -L1 are both within the family Ca. Poseidoniaceae. How many Ca. Poseidoniaceae MAGs were there?
Lines 190-192: CONCOCT and MaxBin2 also use both nucleotide composition and differential coverage to bin contigs, so this alone won’t explain why MetaBAT2 performs best on these samples…
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