The RNA Viruses in Samples of Endemic Lake Baikal Sponges

Round 1

Reviewer 1 Report

The authors put an in deep effort to discuss the plenty of data detected regarding the viruses hosting sponges from lake Baikal. The study is methodologically correct and well written in general. I have only some only suggestion that may improve the outcomes and how they are discussed

 

Please add at least on sentence in the abstract justifying why it is important to study the virome. It is wee defined that there are not many previous available studies but it is important to state what is the importance of studying these communities.

 

In line 28 should it be “phylum” instead of “type”? Please correct

 

The structure of the Introduction should be rearranged. The authors explain well in the scope paragraph the reason why RNA viruses hosting sponges should be studied, however this should be placed before the previous paragraph that presents the short history of metagenomic studies. In this manner better connectivity would be achieved

 

The authors discuss based on their results the stress due to climate change effects. Although, as reported in the discussion, change in HSP70 has been observed in Baikal sponges, in my opinion this cannot explain the difference in RNA viruses diversity. Also I would recommend to add in the discussion the general trend in Baikal regarding temperature and oxygen availability in the context of climate change

 

Finally an interesting question to be discussed is if apart from the different viruses detected in freshwater versus marine sponges in comparison with previous studies, if there is also difference in the diversity in viruses between the two groups. This would be a valuable addition further improving the manuscript

Author Response

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Author Response File: Author Response.pdf

Reviewer 2 Report

I have reviewed the manuscript titled The RNA viruses in the samples of endemic Lake Baikal sponges and have the following comments

1. As many readers are not familiar with the process of obtaining viral particles from living tissue samples it would be necessary to explain in more detail the processes that are in the papers no 14 and 15 [line 89].
2. I would ask the same detail is provided for extraction of viral RNA [also line 89].
3. In Fig 1 the authors should indicate the names and locations of each sponge shown
4. This sentence does not fit well into the paragraph [lines 177-179] ‘Before CCA to equalize the effect of different counts virotype and TPM per sample (from the highest to the lowest ones), the values ranged between 0 and 1.’
5. The Section discusses types of sample pretreatment [line 207 onwards] whereas there was no mention of these additional processes in the Methods section.
6. The depletion of ribosomal RNA   during pretreatment has a significant impact on the levels and types of RNA viruses, but this was not done for these samples. Perhaps this is step would have improved the recovery of RNA viruses  in this study.
7. The healthy and diseased samples showed rather similar identified virus content though the latter had lower levels of virus. Therefore, can one conclude that the diseased status is not primarily as a result of viral pathogens?
8. The Conclusions appear not to correlate with the study, apart from the few Ribivaria identified from the Lake Baikal. 
9. On what basis was the choice of marine sponge virus as comparative samples made? The two samples from Scotland are presumably the only fresh water samples compared to these Freshwater sponge hosts. Yet we do not see any comparison to these freshwater samples.

Author Response

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Author Response File: Author Response.pdf

Reviewer 3 Report

The idea of this paper is very interesting and it is within a very exciting and underexplored area. However, there some methodological points that are very concerning.

1.      In line 116, did you mean paired-end reads?

2.      Which library prep kit did you use? Please, specify it.

3.      You must improve all figures resolution.

4.      I am really concerning about the low sample number given that it does not allow confidence statistical comparisons. Also, you collected samples in different years (2015 and 2018), and it certainly affected the obtained results and, once again, prevent confidence statistical comparisons. In this matter, did you collect physical-chemical parameters of the water, such as pH and temperature? I would be very helpful to improve your analyzes.

5.      I am not sure if the strategy of collecting two branches from the same sponge (healthy and non-healthy) is the better one. Why did you choose this strategy instead of collect from different individuals?

6.      How distance were the sponges you use to collect samples?

7.      You should include in your discussion the importance of the sponges for the surveillance of water pollution. Are the sponges good biomarkers of hospital wastewater pollution in the oceans regarding their RNA viruses?

Extensive editing of English language is required.

Author Response

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Author Response File: Author Response.docx

Round 2

Reviewer 3 Report

Thank you for your answers. You have adressed all my questions. 

Moderate editing of English language required.