Filtering Effect of Rhinogobio cylindricus Gut Microbiota Relieved Influence of the Three Gorges Dam on the Gut Microbiota Composition

Round 1

Reviewer 1 Report

The authors have made all the requested changes as far as I can see.

Therefore, I have only very minor comments at this point:

Line 13: ‘Fish gut microbiota was’ – I think, this should be ‘Fish gut microbiota were’ because microbiota is plural.

Line 13: ‘by the habitat changes’. I think this should be written: ‘by habitat changes’. The article use suggests that the sentence is referring to particular habitat changes. However, the type of habitat changes has not been introduced at this point, thus a generalization may be better here.

 

Line 80: Change ‘endemic Chinese cyprinid fish that specifically distributes in the upper reaches of the Yangtze River and its tributaries’ to ‘endemic Chinese cyprinid fish that is distributed in the upper reaches of the Yangtze River and its tributaries’.

 

Line 172: Change ‘microbiota in the water environment was significantly’ to ‘microbiota in the water environment were significantly’.

 

Lines 193/194: The different lowercase letters on the top of the boxplots indicate that there was a significant difference between the two groups. – Which two groups are meant here? Please clarify.

 

Author Response

Thank you very much for reviewing our paper and providing useful comments. These comments are valuable for us to revise and improve our manuscript. We have revised our manuscript according to your and another reviewer’s comments. The responses to the minor comments are as follows,

Line 13: Thank you for your comment. We have revised our manuscript according to your comment.

Line 13: Thank you for your comment. We have revised our manuscript according to your comment.

Line 80: Thank you for your comment. We have revised our manuscript according to your comment.

Line 172: Thank you for your comment. We have revised our manuscript according to your comment.

Lines 193/194: Thank you for your comment. We have revised the sentence. It should be “The different lowercase letters above the boxplots show the significant differences among the groups (p < 0.05)”. We also revised the description in the legend of the Figure 2.

Reviewer 2 Report

I read through the revised manuscript and the author’s response to the reviewers, in which the authors properly responded to the most comments. However, I still cannot fully understand the “strong filtering” of R. cylindricus gut microbiota that the authors emphasized as the highlight of this study. As I commented, it is no surprise that fish gut microbiota had lower diversity than those of the surrounding environment, because of their filtering systems (as the authors mentioned in line 71, refs 12, 19), therefore I cannot understand the scientific significance of the results in this study. If the authors wish to emphasize that the filtering system of the R. cylindricus gut microbiota was “strong”, they have to clarify how stronger it is comparing to those of other fishes at least. The authors explained that the R. cylindricus gut microbiota showed an “obviously less number” (how much?) of OTUs compared to that of largemouth bass, but this fact is not enough to fully prove their stronger filtering system. Another direction worth discussing is that how the selected bacterial taxa in the R. cylindricus gut potentially benefit their host. The authors explained that R. cylindricus has experienced severe reductions because of the TGD construction (line 81). If this fish was NOT affected by the construction compared to other fishes because of their characteristic strong gut microbiota filtering system, then I would understand the scientific significance of studying their gut microbiota. According to the facts the authors presented, it seems more likely for me that R. cylindricus was severely affected by the TGD construction, because of their “less flexible” gut microbiota structure, which could not adapt to the new habitat environments and food composition created by the TGD construction. The authors concluded that “TGD did not affect the changes in the gut microbiota of R. cylindricus”, but they should rethink more carefully what this fact means.

Author Response

Thank you very much for your enlightening comments. Since we really can’t quantify the filtering intensity, we deleted the word “strong” throughout our manuscript. As you said, there was a possibility that R. cylindricus cannot adapt to the environmental changes caused by the TGD due to their “less flexible” gut microbiota structure, resulting in a significant reduction of R. cylindricus. However, our results implied that the severe reductions of R. cylindricus was not due to the change of their gut microbiota composition caused by TGD, but was likely to be caused by other ways, such as destruction of spawning grounds. However, these conjectures need to be confirmed by further study. We have added some discussion in our revised manuscript. Your enlightening comments prompted us to design new experimental schemes to test these possibilities. Thank you again.

Round 2

Reviewer 2 Report

The authors properly responded to the reviewer's comments, and now the manuscript has been much improved.

This manuscript is a resubmission of an earlier submission. The following is a list of the peer review reports and author responses from that submission.

Round 1

Reviewer 1 Report

1) we found that the water microbiota composition changed regularly according to the distribution of sampling sites upstream of the TGD, but the internal microbiota of R. cylindricus did not show the same pattern.-MY COMMENT- THE CONCLUSION IS TOO GENERALLY AND, IN MY OPINION, IS NOT LOGICALLY LINKED WITH THE AIM OF THE PAPER-  FORMULATED BY TH EAUTHORS Therefore, we hypothesized that although the construction of the TGD would have altered the water environment and the water microbiota, the fish intestinal tract could counteract  the effect of the dam construction on the composition of the gut microbiota in individuals
in the upstream water of the TGD through the bottom-up effect

2) THE COMPLEX ANALYSIS PERFORMED BY THE AUTHORS ARE NOT- at tleast in my opinion, in my logic- DIRECTLY LINKED TO THE DESIRED CONCLUSIONS  OF THE AUTHORS.

Reviewer 2 Report

Review for: Strong filtering of Rhinogobio cylindricus gut microbiota relieved influence of the Three Gorges Dam on the gut microbiota composition

By Chen et al.

The authors present an interesting and timely study on the potential effects of dam construction on fish gut microbiota. This information is important for fish conservation as gut microbiota composition has been linked to, for example, immunity responses. I think, the paper is well written and presented and therefore, I have only minor comments outlined below. I believe, it would be important to clarify if fish specimens are able to pass the dam somehow. If so, this would offer an alternative explanation to why the microbiota diversity appears to be largely unaffected by dam construction. This possibility should be discussed in the paper.

Minor comments:

Line 74: Could you explain the bottom-up effect briefly for readers that are not so familiar with this concept (and probably add a citation for it as well)?

Line 85: what does ARRIVE stand for? Probably also add a link to a website, if possible.

Line 246: Escherichia coli should be written in italic font as it is a species name.

Lines 324 – 326: Here, you write that the species is migratory. I think, the readers would benefit from a bit more background. Is this a species that can pass the dam? Or are there mitigation measures in place to assist migration of this fish (e.g., supportive breeding)? I believe, these pieces of information would add to the reader’s understanding of the system.

Reviewer 3 Report

The MS is interesting and, in my opinion high quality. But before final acceptation MS need some correction. I marked my detailed remarks in MS file in the form of comments.

Comments for author File: Comments.pdf

Reviewer 4 Report

This study by Chen et al. tackled the potential impact of the construction of the TGD on the surrounding river ecosystems, especially focusing on the water microbiota and the gut microbiota of R. cylindricus. The conclusive hypothesis of this study is that the TGD construction “significantly” affected the river water microbiota compositions, while the fish gut microbiota was not affected, because of their “strong” filtering system. However, based on the current results and discussion, readers cannot understand (1) the specific impact of the TGD construction on the geography, water quality, and ecosystems (therefore, the research questions, problems, and motivations were not clear), (2) the “significant” change in the water microbiota, and (3) the “strong” filtering ability of the gut microbiota of R. cylindricus (therefore, the reason why the authors focused on this fish). The authors have to greatly reconstruct the research and improve the manuscript to publish it. Please address the following points.

 

Throughout the manuscript:

The authors used the word “significantly” too much. It is a very strong word and the authors should use it only in case the result was statistically significant.

The genus name must be in italic (Rhinogobio cylindricus in title, Synechococcus, Escherichia coli, …)

 

Line 51: Dam construction may potentially change …

How did the authors expect the dam construction to have affect the fish gut microbiota? It is very unspecific and indirect. The authors should explain first about the actual impact of the dam construction on the water quality and ecosystem (especially fishes) in detail. Therefore the research questions and motivations are unclear in the current version.

 

Line 75:

Why R. cylindricus was chosen to study? Is this species known to have the “strong” filtering system for their gut microbiota comparing to other fishes? Was this species strongly or weakly affected by the dam construction comparing to other fishes? The introduction was poorly written and must be greatly improved.

 

Line 143, Figure 1: “significantly different…”

When comparing the upstream sites and the influenced sites, only TDS and conductivity seemed different, and other parameters did not seem “significantly” different. Please explain in more detail.

 

Line 145:

What is “regular changes”?

 

Line 145: These results indicated the complexity of the river water…

It is too unspecific and did not explain about the results at all.

 

Line 158:

What does “high-quality” mean?

 

Line 167:

It is not surprising that the gut microbiota had lower diversity than the environmental sample. Does this fish species have a “strong” filtering system comparing to other fishes? The authors should explain more about how “strong” it is.

 

Figure 3A-D:

Is it necessary to show all of these plots?

 

Figure 4:

Results are very unclear and difficult to understand. I think the authors should first show the microbial community structures of each site in a bar chart or a pie chart.

 

Line 211-213

I cannot see the “significant” differences between different sampling sites. The authors mentioned Actinobacteria, Chlorobi, and Bacteroides, but their relative abundances seemed very similar in each site.

 

Line 217:

What is “regular pattern”? Should explain much more about the results from the gut microbiota.

 

Line 261: only velocity had a significant effect…

Did the dam construction affect the water velocity? In the end, how did the dam construction affect the environment? Readers cannot understand the whole story.

 

Line 281, Figure 6:

Very hard to accept this “slight but significant positive correlation” result.