Different Assembly Patterns of Planktonic and Sedimentary Bacterial Community in a Few Connected Eutrophic Lakes
, Zhicong Wang 4, Dongdong Zhai 1, Hongyan Liu 1, Yuanyuan Chen 1, Jixin Yu 1 and Ying Wang 1Round 1
Reviewer 1 Report
The manuscript entitled "Different Assembly Patterns of Planktonic and Sedimentary Bacterial Community in a Few Connected Eutrophic Lakes" is highlighting the scope of journal. The research work is very valuable. The topic is very interesting and critical for the field. The research is planned very carefully (in line with scientific standards. The introduction is very comprehensive but needs to be supplemented with more recent literature. The used methods are presented very clarify. The strong point of the research are well-chosen and comprehensive statistical methods which authenticate the presented results.
I did my best to improve your manuscript, but it requires a minor revision. In order to improve of manuscript quality I suggest you consider following comments:
General comments:
Second sentense in the Intruduction is "It is a common concept that there are two distinct habitats known as water column and sediments in a lake because of their totally different environmental conditions". I agree with it, but I would also note to bacterioneuston which is separate habitat too.
In my opinion some sentences eg. "In aquatic ecosystems, it is widely known that bacteria, as the major consumers and transformers of organic substrates, play irreplaceable roles in aquatic biogeochemical cycles" and "In recent years, high-throughput 16S rRNA gene sequencing method has become more and more common recently with the characteristics of acquiring large number of sequence data on microbial communities" need to be supported by more recent literature (see eg. https://doi.org/10.1016/j.ecolind.2020.106335 or https://doi.org/10.3390/su132011518).
I appreciate the graphical form of the results presentation, but I miss raw data for the OTUs for individual sampling sites. You can attach them to supplementary materials.
Figure S2 in the supplementary materials has an incomplete description. I guess that chart A and B presents the results in water and sediment, respectively. By the way, In my opinion that these are some of the basic and valuable results and should be included in the main manuscript.
In point 3.2 you state that "significant linear relationship was found between the species richness and phylogenetic diversity and TSIc in water". Czy R^2= 0.14 can prove the existence of a correlation (the blue lines are flattened) ? Please explain it to me.
I hope you find the above comments helpful. Concluding, in my opinion after minor revision the manuscript can be published in Water journal.
Author Response
Response to Reviewers’ comments
Dear reviewer:
Thank you for the quick review of our manuscript and the valuable comments of the reviewers. Those comments are all valuable and very helpful for revising and improving our paper. We have studied comments carefully and revised our manuscript according to the reviewer(s)’ comments. Detailed below are the corrections made to our manuscript entitled“Different assembly patterns of planktonic and sedimentary bacterial community in a few connected eutrophic lakes” By Xia et al. Revised portion are marked in red in the paper. Changes made in the manuscript are as the follows:
Reviewer 1:
Comment: Second sentense in the Intruduction is "It is a common concept that there are two distinct habitats known as water column and sediments in a lake because of their totally different environmental conditions". I agree with it, but I would also note to bacterioneuston which is separate habitat too.
Response: Thank you for your valuable comment. According to your suggestion, we have added bacterioneuston as a separate habitat in lakes to improve the introduction.
Comment: In my opinion some sentences eg. "In aquatic ecosystems, it is widely known that bacteria, as the major consumers and transformers of organic substrates, play irreplaceable roles in aquatic biogeochemical cycles" and "In recent years, high-throughput 16S rRNA gene sequencing method has become more and more common recently with the characteristics of acquiring large number of sequence data on microbial communities" need to be supported by more recent literature (see eg. https://doi.org/10.1016/j.ecolind.2020.106335 or https://doi.org/10.3390/su132011518).
Response: Thank you for your valuable suggestion, we have added the two recent literature.
Comment: I appreciate the graphical form of the results presentation, but I miss raw data for the OTUs for individual sampling sites. You can attach them to supplementary materials.
Response: Thank you for your valuable comment. We have submitted raw data of the OTUs in every sampling site on the NCBI (PRJNA777015 is for water and PRJNA777413 is for sediment), and I also have referred it in manuscript.
Comment: Figure S2 in the supplementary materials has an incomplete description. I guess that chart A and B presents the results in water and sediment, respectively. By the way, In my opinion that these are some of the basic and valuable results and should be included in the main manuscript.
Response: Thank you for your valuable comment. According to your suggestion, we have completed the figure S2 and added it in the main manuscript (merged with figure 4).
Comment: In point 3.2 you state that "significant linear relationship was found between the species richness and phylogenetic diversity and TSIc in water". Czy R^2= 0.14 can prove the existence of a correlation (the blue lines are flattened) ? Please explain it to me.
Response: Thank you for your valuable comment. Your suspicion is quite correct. Czy R^2= 0.14 is too weak, “Significant but weak” might be a more reasonable statement. So the relationship has been changed to “significant but weak” in the manuscript.
Author Response File: 
Author Response.pdf
Reviewer 2 Report
The manuscript submitted by Xia and colleagues investigate the bacterial community of water and sediment sampled in five connected eutrophic lakes, to individuate the processes and the factors determining the community composition.
Although the central topic was addressed, the manuscript needs to be improved and specific comments have been included in the revised version of the manuscript (see the attached file).
- English should be revised. In addition, various sentences are not clear enough and should be re-written.
- There are a number of typing (i.e. no spaced words and many others) and grammar errors along the whole manuscript.
I highlighted just some of them, but a careful revision is required.
- Materials and methods lack some information.
- Some figures and figure captions need to be revised
- A discussion with results reported in the literature for similar environments is missing. If possible, the authors should provide a comparison with the literature about the parameters acting on bacterial community composition and structure in eutrophic lakes.
Comments for author File: Comments.pdf
Author Response
Response to Reviewers’ comments
Dear reviewer:
Thank you for the quick review of our manuscript and the valuable comments of the reviewers. Those comments are all valuable and very helpful for revising and improving our paper. We have studied comments carefully and revised our manuscript according to the reviewer(s)’ comments. Detailed below are the corrections made to our manuscript entitled“Different assembly patterns of planktonic and sedimentary bacterial community in a few connected eutrophic lakes” By Xia et al. Revised portion are marked in red in the paper. Changes made in the manuscript are as the follows:
Reviewer 2:
Comment: English should be revised. In addition, various sentences are not clear enough and should be re-written.
Response: Thank you very much for your suggestions on the language problems in the manuscript. According to your suggestion, we have asked native English researcher in related fields to help us revise the manuscript. We also read the article carefully and improved many language and semantic expressions.
Comment: There are a number of typing (i.e. no spaced words and many others) and grammar errors along the whole manuscript. I highlighted just some of them, but a careful revision is required.
Response: Thank you very much for reviewing our manuscript carefully and pointing out many language mistakes and grammar mistakes in the manuscript carefully, we have tried our best to correct them one by one in the manuscript. A native English researcher in related fields also helped us revise it.
Comment: Materials and methods lack some information.
Response: Thank you for your valuable comment. According to your suggestion, we have added the DNA extraction protocol in “materials and methods” section and the reference of primers. dNTP concentration also has been improved.
Comment: Some figures and figure captions need to be revised
Response: Thank you for your valuable comment. According to your suggestion, we have revised some figures and figure captions: 1, “table S2” in the manuscript has been revised to “table S1”; 2, “α-diversity” has been uniformed in the whole manuscript; 3, the text information and color in figure S2 and related figure captions has been revised, and the figure S2 has been moved from the supplements to the manuscript according to the comment of another reviewer; 4, we have placed the sample label at the right side respect to the symbol in figure 5 to better visualize the samples according your suggestion; 5, In the figure captions of figure 7 and corresponding section in the manuscript, we have revised the terminology to “a bacterial diversity variation explained by spatial or environmental variables”.
Comment: A discussion with results reported in the literature for similar environments is missing. If possible, the authors should provide a comparison with the literature about the parameters acting on bacterial community composition and structure in eutrophic lakes.
Response: Thank you for your valuable comment about adding a comparison with the literature about the parameters acting on bacterial community composition and structure in eutrophic lakes. Thank you for pointing out our careless omission in writing. We have added literature showing that the N/P ratio tended to play a vital role in bacterial communities in eutrophic lakes, and CODMn and NH4+-N were the most important environmental parameters in driving the bacterial community of rivers around eutrophic Chaohu lake. In our manuscript, NO3-N, NH4+-N, PO43-, and CODcr were the important environmental factors that affect the bacterial community assembly in water column of five eutrophic lakes. Above all, the nutrient elements played an important role in the composition of phytoplankton communities in eutrophic lakes.
Author Response File: Author Response.pdf
Round 2
Reviewer 2 Report
The manuscript was revised accordingly the comments. However, just some minor improvements/revisions are still needed.
The authors can find the comments in the attached file.
Comments for author File: Comments.pdf
Author Response
Dear reviewer:
Thank you for the quick review of our manuscript and the valuable comments of the reviewers. Those comments are all valuable and very helpful for revising and improving our paper. We have studied comments carefully and revised our manuscript according to the reviewer(s)’ comments. Detailed below are the corrections made to our manuscript entitled“Different assembly patterns of planktonic and sedimentary bacterial community in a few connected eutrophic lakes” By Xia et al. Revised portion are marked in red in the paper. Changes made in the manuscript are as the follows:
Reviewer 2:
Comment: The manuscript was revised accordingly the comments. However, just some minor improvements/revisions are still needed.
Response: Thank you for your valuable comment. According to your suggestions, we have revised the “prime” to “primer”, and added the missing information (The platform and the instrument used for the sequencing was illumina novaseq6000 and the length of reads was PE250) in the “Bioinformatics analysis” section. Thank you very much again for reviewing our manuscript carefully and pointing out the shortcomings.
Author Response File: Author Response.pdf
