PONE-D-20-16591

Woeseiales transcriptional response in Arctic fjord surface sediment

PLOS ONE

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Reviewers' comments:

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Reviewer #1: Yes

Reviewer #2: Yes

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2. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #1: Yes

Reviewer #2: Yes

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Reviewer #1: Yes

Reviewer #2: Yes

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Reviewer #1: Yes

Reviewer #2: Yes

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5. Review Comments to the Author

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Reviewer #1: This a well designed, performed, and written study tracking the genomic diversity and metabolic activity of bacteria through fjord sediments. I have no issues with it in its current form and think it should be published.

Reviewer #2: This manuscript examines five novel metagenome assembled genomes (MAGs) from the Order Woeseiales, a bacterial clade which is abundant in marine sediments, coupled with depth-resolved metatranscriptomic data, from four sampling sites in Arctic fjord surface sediment. The authors report that these MAGs had the capability for chemoautotrophic carbon fixation via the Calvin-Benson-Bassham pathway, coupled to the oxidation of sulfite or thiosulfate, as well as the ability to reduce nitrite to nitric oxide. At three of the four sampling sites, transcription of most of the central metabolism genes dropped with sediment depth, while the transcription of a single gene, spore protein SP21, rose sharply. The authors propose that the Woeseiales in this environment may enter a quiescent state with burial, allowing these microbes to ride out stressful conditions by entering dormancy, only to be revived when improved conditions present themselves (if, for example, they are brought to the surface of the sediment through bioturbation).

While it is risky to extrapolate data from five MAGs to describe the metabolic capabilities of an entire clade, the power of the data presented in this manuscript lies in the coupling of the data to the metatranscriptomes. In this way the authors demonstrate how the Woeseiales found in their samples might survive changing conditions with sediment burial.

The science presented here is well-executed and the manuscript well-written. The methods are logical, well-explained, and justified. I found very little to criticize, but I do have a few minor points:

The authors state towards the end of the discussion that SP21 increased with depth at three of the four sampling sites where they were able to generate metagenomes/metatranscriptomes, and that at the one site where they did not observe this, they also did not observe a concurrent decrease in the abundance and diversity of cellular transcripts. (I assume from the figures that the outlier site is site AC, although this is not stated in the text.) Do the authors have any insight into why this site may be different from the others? Could there be some geochemical parameter at play here? There may of course be no obvious explanation, but a comment or two about what may be driving this difference would be useful.

Line 454 (methods): "extracted by both the Lloyd" is a phrase missing here? Do you mean "both the Lloyd and the Loy labs"?

Figure 5: Some of the depths appear to be missing from sites AB and AC (unless I misinterpreted something in the text). The figure legend mentions that certain libraries from site F were not included- at first it was difficult to tell that points were missing from the line graph at the bottom of the figure, but I can see that those are not there. What happened with the data from sites AB and AC?

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Reviewer #1: No

Reviewer #2: Yes: Lauren M Seyler

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Woeseiales transcriptional response to shallow burial in Arctic fjord surface sediment

PONE-D-20-16591R1

Dear Dr. Buongiorno,

We’re pleased to inform you that your manuscript has been judged scientifically suitable for publication and will be formally accepted for publication once it meets all outstanding technical requirements.

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Kind regards,

Peter R. Girguis, Ph.D.

Academic Editor

PLOS ONE

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