Dynamics of Phyto- and Bacterioplankton in Southern Baikal and Irkutsk Reservoir During the Open Water Period of 2023 According to Metabarcoding Data

Round 1

Reviewer 1 Report

Comments and Suggestions for Authors

In the peer-reviewed manuscript ‘Dynamics of phyto- and bacterioplankton in Southern Baikal and Irkutsk Reservoir during the open water period of 2023 according to metabarcoding data’ by Y. Galachyants et al. presented data on the study of bacterioplankton by metabarcoding of 18S and 16S rRNA gene fragments.

Reviewer comments:

The Introduction section does not describe the aims and objectives of the study. Lines 83-95 of the Introduction section briefly describe the results, but what was the purpose and scientific/academic value of the research carried out? The Abstract needs to be improved in this respect as well.

The manuscript provides a good description of the data collected. In the results section, the authors have presented the data visually well. The data have been processed using modern statistical methods. However, the data analysis seems to be very weak, the discussion section is minimal. In fact, this section briefly repeats the results, with a weak literature analysis of previous studies. It would be appropriate here to provide a literature analysis of previous bacterioplankton studies using other methods to explain what results have been obtained by other researchers of this water body who have studied the reservoir since its early years.

In the Conclusions section, the first and last paragraphs are abstract, generalised reasoning that does not relate to the results of the paper. The first paragraph is exactly the same as the Abstract section. The last paragraph would be more appropriate in the introduction. The conclusions do not answer the question: What is the scientific significance of the study? The study of the seasonal dynamics of bacterioplankton, the conclusions that the bacterioplankton of the reservoir is subject to seasonal changes and is habitat dependent, cannot be a new or scientifically significant result.

The results presented in this manuscript are a small part of a larger project. Data on hydrochemistry, hydrology and phytoplankton have been published in [19,20,21], as indicated by the authors. The map scheme of the work area duplicates previous work; the results relating to the phytoplankton community and hydrochemical parameters repeat previously published material. As the manuscript has no significant scientific value, it is more appropriate to present it as a Communication rather than an Article: Communications are short articles that present groundbreaking preliminary results or significant findings that are part of a larger study over multiple years. They can also include cutting-edge methods or experiments, and the development of new technology or materials. The structure is similar to an article.

Comments on the Quality of English Language

In the peer-reviewed manuscript ‘Dynamics of phyto- and bacterioplankton in Southern Baikal and Irkutsk Reservoir during the open water period of 2023 according to metabarcoding data’ by Y. Galachyants et al. presented data on the study of bacterioplankton by metabarcoding of 18S and 16S rRNA gene fragments.

Reviewer comments:

The Introduction section does not describe the aims and objectives of the study. Lines 83-95 of the Introduction section briefly describe the results, but what was the purpose and scientific/academic value of the research carried out? The Abstract needs to be improved in this respect as well.

The manuscript provides a good description of the data collected. In the results section, the authors have presented the data visually well. The data have been processed using modern statistical methods. However, the data analysis seems to be very weak, the discussion section is minimal. In fact, this section briefly repeats the results, with a weak literature analysis of previous studies. It would be appropriate here to provide a literature analysis of previous bacterioplankton studies using other methods to explain what results have been obtained by other researchers of this water body who have studied the reservoir since its early years.

In the Conclusions section, the first and last paragraphs are abstract, generalised reasoning that does not relate to the results of the paper. The first paragraph is exactly the same as the Abstract section. The last paragraph would be more appropriate in the introduction. The conclusions do not answer the question: What is the scientific significance of the study? The study of the seasonal dynamics of bacterioplankton, the conclusions that the bacterioplankton of the reservoir is subject to seasonal changes and is habitat dependent, cannot be a new or scientifically significant result.

The results presented in this manuscript are a small part of a larger project. Data on hydrochemistry, hydrology and phytoplankton have been published in [19,20,21], as indicated by the authors. The map scheme of the work area duplicates previous work; the results relating to the phytoplankton community and hydrochemical parameters repeat previously published material. As the manuscript has no significant scientific value, it is more appropriate to present it as a Communication rather than an Article: Communications are short articles that present groundbreaking preliminary results or significant findings that are part of a larger study over multiple years. They can also include cutting-edge methods or experiments, and the development of new technology or materials. The structure is similar to an article.

Author Response

Please see the attachment.

Author Response File: Author Response.pdf

Reviewer 2 Report

Comments and Suggestions for Authors

1. Line 169-181：In view of the differences in species composition between SB and IR mentioned in this paragraph, it is suggested that some specific examples can be given.
2. This study mainly focused on the microbial communities of SB and IR, but the relationship between these microbial communities and local ecosystem services and human health was less discussed. It was suggested that the authors could add this aspect in the discussion section to correspond to the "service to the local population" mentioned in the abstract.
3. The language in this article is very fluent, but it is important to carefully check for any issues with expression and formatting.
4. The purpose and significance of the study were not specified in the Abstract.
5. The figures in the paper were not clear enough. It is suggested that both the text and figures be centered within the page and text box for better formatting.

Author Response

Please see the attachment.

Author Response File: Author Response.pdf

Reviewer 3 Report

Comments and Suggestions for Authors

The manuscript by Galachyants and co-authors presents an interesting study on the seasonal dynamics of two connected freshwater bodies in the southern part of Lake Baikal. The study, conducted using 16S/18S metabarcoding, is undoubtedly an important contribution to future monitoring of the ecological status of water bodies in the Baikal region. In this work, the authors used an approach based on parallel metabarcoding of the V3-V4 hypervariable region of 16S rRNA and the V8-V9 region of 18S rRNA. This approach allows the study of both prokaryotic and eukaryotic fractions of the water column microbial community. At the same time, it is not possible to estimate the ratio between pro- and eukaryotes based on these data, which is generally a major drawback of this approach.

In general, the manuscript is well written, most of the methods are described in detail, and the results are presented in sufficient and sometimes too much detail (some of the tables can be moved to Supplementary materials). There are also some comments on visualization and discussion of the dynamics of taxonomic composition.

In general, the research provides valuable insights into the structure and diversity of phytoplankton and bacterioplankton communities, highlighting their seasonal variations and the influence of environmental factors. The study is well-structured and methodologically sound, but certain aspects could be improved to enhance clarity and conciseness.

The following are comments on specific sections of the manuscript:

1. INTRODUCTION:

1-01. lines 48-54. As stated above, parallel metabarcoding of 16S and 18S rRNAs does not provide information on the complete structure of the microbial community, but only on the composition of the separately prokaryotic and separately eukaryotic parts. The only solution to this is shotgun metagenomics, which is a much more expensive experiment and therefore much less widely used. In order for the reader to understand the essence of the experiment, I think it is fundamentally important to disclose this question in more detail.

1-02. lines 94-94 Please state that microscopic results of the same samples were published previously.

2. M&M

2-01. lines 113-115. Please specify the filtration method and the device used for filtration. Was it vacuum filtration, was a peristaltic pump used, or was the water filtered by gravity?

2-02. lines 117-120. The Rusch protocol describes DNA isolation directly from the filters, whereas in this paper it appears that isolation was performed from biomass washed from the filters in a volume of 10 ml. Please describe the biomass concentration procedure in more detail.

2-03. Table 1. The authors have presented a large Table 1, which contains only technical information about the processing of the reads. I propose to move it to the Supplementary Materials so as not to complicate the perception of the manuscript.

3. RESULTS

3-01. line 160. “For exploratory analyses, ASVs with a read count above 50 were selected…” I think that should be 50 thousand reads?

3-02. lines 203-208. The authors describe differences in the behaviour of different alpha diversity metrics (Shannon/Simpson vs. ACE), but do not attempt to explain this either in the results section or further. Given the properties of the ACE index, which is extremely sensitive to rare species, this observation deserves at least some discussion.

3-03. Figure 2 and 3. The division of the figure into three horizontal panels by month is not very clear. This makes it difficult to perceive the figure and it becomes difficult to visually inspect the presence/absence of seasonal dynamics. I would suggest simplifying the figure as much as possible by visualizing the averages for each experimental group as a bar chart on one horizontal panel.

3-04. In general, the sections “Taxonomic composition and dynamics of prokaryotic/micoreukaryotic communities” lack the relative abundances in the text, which should be beneficial at least in some cases.

3-05. Figure 6. The figure 6 lacks the color legend.

3-06. Figures 7 and 8. The heatmaps of 100 top taxa are beautiful, but completely unreadable. I would suggest to decrease the number of shown taxa to 40 and, possibly, to add the informations about the abundance of not visualized taxa as a separate row. Also, the names of zOTUs are not informative. Please, add the genera names.

3-07. The section “Dynamics of cyanobacterial abundance” seems to be disconnected from the main text. It would be useful to integrate it into the section "Taxonomic composition and dynamics of bacterioplankton communities". The same concerns the section “Dynamics of diatom abundance…”.

4. DISCUSSION

4-01. lines 452-463. In the Discussion section, the authors compare their results with metabarcoding results from the Kuibyshev reservoir in the Volga basin. It is not very clear what lies behind the choice of the object of comparison. Is it just the uniformity of the research methods or some characteristics of the reservoirs? It would be desirable to justify the object of comparison.

5. CONCLUSIONS

5-01. The Conclusions section is too long, which is not in line with the authors' guidelines. It is suggested that most of the Conclusions section be incorporated into the Discussion section or simply reduced to one or two paragraphs.

Author Response

Please see the attachment.

Author Response File: Author Response.pdf

Round 2

Reviewer 1 Report

Comments and Suggestions for Authors

The authors made sufficient and appropriate changes to the manuscript. The manuscript may be accepted in its present form.

Reviewer 3 Report

Comments and Suggestions for Authors

I would like to thank the authors for their hard work in producing a much clearer and more readable manuscript. I also generally agree with the authors' extensive comments, in which they explain their approach to presenting the material.

Overall, the manuscript has improved significantly as a result of the revision, and I believe it is ready for publication in Diversity.