Isolation of a Novel Thermophilic Methanogen and the Evolutionary History of the Class Methanobacteria

Round 1

Reviewer 1 Report

 

Dear authors and editors,

 

The accumulation of new knowledge about methanogens contributes to the understanding of the evolution of living organisms. Methanogens  can also be a promising source of enzymes with unique properties for biotechnological use. Therefore, I believe that the description of a new strain of the genus Methanothermobacter  may be interesting to readers, and the article has novelty and scientific significance. The materials and methods of the study are described in detail, the results are qualitatively visualized.  After reading the article, I had two questions.

 

1. The article consists of two parts. This is a description of a new strain (biological species) and modeling of evolutionary relationships within the class Methanobacteria. Has the study of a new strain changed the understanding of the evolution of this class? What specific contribution has it made to this area? It seems to me that a brief description of this in the discussion would increase the value of the article.

 

2. The TOF-SIMS method is not standard for studying microbial cells, although in some articles it has been used for this purpose.  What kind of new information about the strain cells was obtained using TOF-SIMS? Was it possible to draw important conclusions based on it?  I think this is worth focusing on in the article. This will be of interest to researchers who plan to use this method.

 

Author Response

Please see the attachment

Author Response File: Author Response.docx

Reviewer 2 Report

General comments:

The manuscript by Lv et al. describes the isolation of a novel thermophilic methanogen and the evolution of the class Methanobacteria based on genome information. The manuscript is relatively clear written, but there are some points that would need changes. The text is good to read but it would be good to give it either to language service or a colleague that is basically native speaker. There are common mistakes with using the word “the” too many times and at the wrong places. I will give some examples in the specific comments, but will not list all of them. The species name has not the correct ending in my opinion, it should read “tengchongensis” as in “marburgensis”. But please double check this with an expert taxonomist. Some details are repetitive, also in the figure legends. I will give examples in the specific comments. Another point is that I find the map used by the authors to be at least discussable as the borders drawn in the picture represents the official view of the government of the People’s Republic of China, including Taiwan and the area of the Paracel and Spratly Islands but that is not the view of the majority of the rest of the world. I suggest to use a more neutral map section.

 

Specific comments:

Title: Please replace “new” with “novel” and change throughout the manuscript (MS).

Line 14: Delete “ancient” as this word is too imprecise/vague here. In my opinion all the classes are ancient…

L76-79: This can be deleted as it repetitive to the sentences right above.

L101: Please use the scientific writing g L-1. Change this throughout the MS.

L118: Why did you use double distilled water as blank for the growth measurements at 600 nm? The strain does not grow in distilled water, no? So, it should have been the medium used as blank.

L125: “was” instead of “were”.

L152: “using” instead of “by”

L154: How did you measure the DNA concentration, please include. Write “integrity” instead of “integrality”.

L155: Delete “of pure culture”. It is clear that it means the isolate.

L158-159: Delete “For predicting the none-coding RNA”.

L163: I would set the bracket after “repeat” and delete the one after “sequences” as it is the CRISPR sequences.

L169: Write “…from the four…”

L173: Delete “the algorithm” as MAFFT is a program. Delete “and”.

L174: Combine the sentences by “and” and delete “Then 37 marker genes were” to shorten it.

L179: Replace “Then another” with “A”.

L191: Write “gene sets” and check throughout the MS.

L196: Delete “The” and replace “one” with “a”.

L201: Which potential methanogenesis substrates were used? Please include.

L204: Delete “the” before bicarbonate. This is an example of using the article too many times and in the wrong way as there should be no article.

L211: Write “continuous” and “were” instead of “are”.

Fig. 1B: If you want to keep the text in the picture, please move it to the bottom and write “Temp.”. Also shorten the figure legend as much of it has been already written in the main text. Avoid repetition.

L221: Delete both “the”. Another example of using “the” the wrong way.

L222-224: Start with “Strain”. Keep words only until “microscope” and then “Fig. 2A.”, because you have already written in detail what light source and so on in the methods section. Again, avoid repetition.

L230: Write “did not” instead of “didn’t”, change throughout the MS, also for “can’t”. Write “…observe a flagellum (Fig. 2B-D),…”

L233-235: You should delete this sentence.

L239-240: Delete this sentence, it is repetitive.

Fig. 2E-G: The darker parts in the pictures are cell aggregates? If so, please add that information to the figure legend, it helps to understand.

L246: Delete “of DL9LZB001”

L248: Write like that “=3). No growth was observed at…”

L252: Delete “of the cultures” and write “pH 6-8”

L257-258: This sentence can be deleted.

Table 1: For cell size, please replace the star sign “*” with a “x”. I would not leave blank space in the table, but write for example “n.d.” “not determined”. Otherwise it looks as if you have forgotten to fill in a value, no matter you explained it below.

L293: Do you mean “DPANN”? Check throughout the MS.

L294: “superphylum”

L302-303: Change maybe like that “…species, that was named XXXX”.

Fig. 5: DPANN?

L315: Delete “And”, start with “Then”.

L317: “dehydrated” and replace the “and” with a comma.

L324: “During the above process…”

Fig. 6: Please use thicker lining, it looks a bit faint and the purple coloration is also not well visible.

L345: Delete “value is”.

L351: I assume you mean that it could oxidize thiosulphate as you know only the genomic potential but not if the strain can do that in reality, no? Or did you test the strain for thiosulphate oxidation?

L353: “uptake of”

L358-359: Write “A phylogenetic tree was constructed and…”

L386: “Star” instead of “pentacle”?

L387: What do you mean by “underwater”? Groundwater?

L389: “ellipse” instead of “roundness”

L391: “sign”, not “sigh”

L396: “were” instead of “are”

L398: “diverging”. Replace “and then” with “followed by”.

L399: “of the members”

L400: “speculate”

L402: “to a mesophilic”

L408: “suggest”

L413: “…may be related..”

L416: “…adapt to thermal..”

L418: Delete “rest”.

L428: Replace “the” with “for”.

L432: “…gaining these genes…”

L441: “…did not experience a large gene gain…”

L445: The part with methanol trophic sounds strange, please check and rewrite.

L446: “research”

L451: Better use “may” instead of “should”.

L471: what do you mean with “hugged for”? I don’t understand that.

L471-473: The last sentence of the conclusion should be deleted as it is a filling sentence.

Author Response

Please see the attachment

Author Response File: Author Response.docx