PONE-D-21-15605

Giant sulfur bacteria (Beggiatoaceae) from sediments underlying the Benguela Upwelling System host diverse microbiomes

PLOS ONE

Dear Dr. Flood,

Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we feel that it has merit but does not fully meet PLOS ONE’s publication criteria as it currently stands. Therefore, we invite you to submit a revised version of the manuscript that addresses the points raised during the review process.

Both reviewers and I think the paper reports new and interesting findings about the Beggitoa microbiome. The reviewers  indicated that the manuscript could be suitable for publication, provided their comments are responded to adequately. In addition to theirs, I suggest a minor editorial comment: on line 31, I think it would be better to say that they were "pooled by morphotype for community analysis" or something similar; the goal of the iTag sequencing is more important than the approach.

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PLOS ONE

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Reviewers' comments:

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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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Reviewer #2: Yes

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Reviewer #1: The paper “Giant sulfur bacteria (Beggiatoaceae) from sediments underlying the Benguela Upwelling System host diverse microbiomes” authored by Beverly Flood, Deon C. Louw, Anja K. Van der Plas and Jake V. Bailey is devoted to ecological study of microbial communities on the coast of Namibia, where abundant aggregation by bacteria from the family Beggiatoaceae occurs. The authors pay special attention to the composition of communities associated with mucous formations around sulfur bacteria from the family Beggiatoaceae. The authors investigate the geochemical characteristics of water at the sampling sites. To determine the taxonomic composition, the authors sequenced the V4 region of 16S rRNA from the samples.

The authors make a conclusion about metabolic potential of organisms associated with Beggiatoaceae on the basis of the taxonomic composition. These miroorganisms interact with each other through syntrophic exchange of H 2 and acetate produced as the result of Beggiatoaceae sheath fermentation, as well as products of sulfur and nitrogen compounds metabolism.

It is interesting that there are no anaerobic ammonium-oxidizing bacteria (annamox) among Beggiatoaceae-associated microorganisms. But authors suppose that anaerobic/miroaerobic lithotrophic ammonium oxidation could be coupled with either iron (ferromox), sulfate (sulfammox) or thiosulfate (sammox) respiration and/or heterotrophic nitrification as well as denitrification could be occurring.

The work was carried out at a high scientific and methodological level. A large amount of data was obtained, and the authors managed to analyze and structure these date. All results seem to be good and valid. There are some minor comments and corrections on the article:

L. 88: i.e. should not be written in italic. Commas after Beggiatoa spp. and Ca. Isobeggiatoa spp. are needed

Please, delete comments from S1 Text

L. 266: ‘Thioflexithrix’, not ‘Thioflexothrix’. It is interesting that ASVs from marine sediment can be classified as Thioflexithrix, because originally described Thioflexithrix psekupsensis was isolated from freshwater habitat. it might be worth discussing this fact.

L. 485: it may be worth mentioning that the opportunity of Beggiatoaceae assotiation with Spirochaeta was already shown (Grabovich et al., 2021 DOI: 10.1016/j.biosystems.2020.104322)

L. 521: Thiomargarita should be written in italic

Ref 25. Leptomitoformis should be written with a lowercase letter

Reviewer #2: This manuscript, exploring the diversity of Beggiotoa and their symbionts in sediments off the coast of Namibia, was very interesting and pleasurable to read. The findings were well-presented and supported by the data. I have only a few minor comments, mostly concerning grammatical corrections which I feel will improve the clarity of the text.

line 91: "way" should be "away" (I believe)

line 98: remove "But"

line 122: remove "But"

line 132: add hyphen to make it "Beggiatoaceae-dominated"

line 133: remove hyphen to make it "sulfate reduction"

lines 272-274: Is "introns" the correct term here? I was not aware that introns were found in prokaryotic genomes. Also, "which is" should be changed to "which are," if you are referring to multiple introns.

lines 438-450: "Significantly associated" should be further defined here. How does DESeq2 make this determination (I assume with statistical analyses but if so, which ones).

lines 525-527: This sentence is somewhat confusing- consider rephrasing.

line 534: remove "But"

line 535: change "thus" to "and thus"

line 555: "one ASV" but then two orders are named. Does this mean one ASV from each order?

line 706: replace comma after "bacteria" with a colon

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Reviewer #1: No

Reviewer #2: Yes: Lauren M Seyler

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Giant sulfur bacteria (Beggiatoaceae) from sediments underlying the Benguela Upwelling System host diverse microbiomes

PONE-D-21-15605R1

Dear Dr. Flood,

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,

John M. Senko

Academic Editor

PLOS ONE

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