Marine Bacterial Communities in the Xisha Islands, South China Sea
Round 1
Reviewer 1 Report (New Reviewer)
In subsection 3.2. the raw and the clean tags for each sample should be indicated in an additional file, while within the text it is better to give the median values for the surface and bottom samples which will be much more informative.
Author Response
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Reviewer 2 Report (New Reviewer)
Comments for author File: 
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Author Response
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Reviewer 3 Report (New Reviewer)
This paper represents a systematic classification of bacterial communities for the coastal zone of the archipelago. The information obtained is useful for understanding the mechanisms of marine biological production. The survey and analysis methods are orthodox and reliable. However, the classifications based on the statistics analysis for survey areas are different, and the explanation of the differences is lacking. This makes the flow of the authors' discussion difficult to understand. In addition, there are scattered areas where explanations are lacking, Figs are not included in the text, and Figs are incomplete. The present study is based on the results of only one survey. In the discussion, the general findings are applied to the area of this survey. However, the mechanism of biological communities and production has unique characteristics for each status, and the study area is also highly unique to the region. Unnecessary or arbitrary considerations should be omitted as much as possible, and a discussion based on the results obtained is sufficiently valuable. By modifying these points, the value and evaluation of this study will be enhanced.
The specific points raised are listed below.
1) L108
The only microorganisms that can be recovered are free bacteria that are not attached to the suspension. The biomass of bacteria attached to the suspension is considered to be high. Please explain why this study does not target bacteria derived from suspended solids.
2) L199
Salinity is an important indicator of water mass mixing. The salinity of each sample should be accurately analyzed and the condition of the water mass should be considered.
3) Fig. 2
The description and units for the vertical axis are missing.
4) L203
Only Simpson in Fig. 3D shows a trend that differs significantly from the other analyses; the reason for the large difference in the diversity of R2 and R3 should be indicated.
5) Fig. 5
Displayed character size of Fig. 5 bar is too small. It is an important description, so the text should be larger and clearer.
6)Fig. 6
When Fig.6 is related to Fig.5, it is easier to understand that the phylum classification color is unified.
7) Fig. 7
The text explaining the figures is too small to read. Diagrams should be clearly displayed. All figures should be revised for clarity throughout the paper.
8) Fig. 8, 9, 10
The figures are missing in the text. The insertion position of figures and its relationship to the text should be indicated correctly.
9) L364-365
Surface currents is able to be analyzed from the distribution of salinity.
10) L367
The reason for the low pH of 7.75 should be discussed.
Author Response
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Round 2
Reviewer 2 Report (New Reviewer)
Comments for author File: Comments.docx
Author Response
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Reviewer 3 Report (New Reviewer)
The revised paper has been appropriately revised to reflect the points raised. The paper is judged acceptable for publication.
Author Response
Thank you very much for your review. Your suggestions have been tremendously helpful in improving our manuscript. We sincerely appreciate you taking the time to provide comments on our article.
Round 3
Reviewer 2 Report (New Reviewer)
1. Some figures still contain bright colors such as figure 6, figure 8 with a red color. It could be replaced by a light color combination.
2. Reference section containing the first three authors only, but it should contain all the authors’ names.
Author Response
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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
The manuscript analyzed the composition and potential function of bacterioplankton communities in shallow coral reef areas of the Xisha Islands.
The manuscript might be published in Diversity after major revision. Please find below some suggestions and comments:
1. The authors found that the diversity of bacterial communities varied significantly among different regions. Proteobacteria (38.58-62.79%) were the most abundant in all sampling sites, followed by Cyanobacteria (15.41-37.28%), Bacteroidota, Thermoplasmatota and Actinobacteriota. By analyzing the composition and potential function of bacterioplankton communities in the Xisha Islands’ coral reef areas, this study reveals differences in bacterial community diversity among regions and factors affecting their distribution. These findings enhance our understanding of prokaryote diversity and roles in this coral reef ecosystems, and be able to provide a basis for their protection and management.
2. The authors explained that the Xisha Islands’ marine environment is influenced by the Asian monsoon, landform and mesoscale. In July and August, southwesterly winds from the East Asian monsoon control surface currents and nutrient distribution. How far the sampling sites off the coastline? Is it possible the authors provide a nearshore ocean current vector map for the reach area? Is it possible to connect the physical environments among these four sampling areas?
3. The authors stated that the marine environment of the Xisha Islands is affected by factors such as the Asian monsoon, landform and mesoscale. During July and August, surface currents and nutrient distribution are controlled by southwesterly winds from the East Asian monsoon. How far away from the coastline are the sampling sites? Can the authors provide a map of nearshore ocean current vectors for the study area?
4. The bacterial communities in four different areas showed significant differences based on four indexes (Chao1, ACE, Shannon and Simpson). Non-metric multidimensional scaling (nMDS) in two dimensions revealed a clear separation of microbiota communities by region. The authors suggest that environmental factors such as pH, temperature, salinity, dissolved oxygen and nutrients play a crucial role in regulating microbial distribution. The sampling depths were relatively shallow (between 1.4 to 9.7 m). What is the situation of the other benthic biological community at the sampling regions? Is it possible to establish a connection between the physical environments and benthic biological community of these four sampling areas?
5. The sampling period of July and August in 2020 may not be sufficient to accurately represent the overall bacterial community in the Xisha Islands.
Author Response
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Reviewer 2 Report
The authors described bacterial community composition in different sites from South China Sea in correlation with environmental parameters and prediction of functional pathways.
Although the overall scope of the study is interesting I have several concerns regarding the methodological stringency of the final output.
1. the quality of english language, mostly in terms of grammar, needs to be imroved.
2. FAPROTAX is not included in methods, and suddenly some functional predictions appear in the results
3. Ranges for physicochemical parameters should be on a table an not in the text since this is tiring for the reader.
4. The authors mention in the methods that 8 samples were lost from DNA extraction and that ended up with 88 samples and finally in the results mention that they got results from 96 samples.
5. The authors apparently merged their results from surface and bottom but they do not mention it anywhere in the text. The nmds shown in Figure 4 shows all samples without mentioning different depths while all graphs regarding taxa have merged results.
6. In paragraph 3.4 (results) it is mentioned that diversity indices were not different between depths but results regarding taxonomic diversity show significant differences. This shows that the authors should have analyzed different depths separately. Also this statistical analysis should have been performed for all sites separately.
7. This lack of statistical stringency influences the quality of all results presented including also functional predictions
8. Last but not least the authors should submit thei results in a public database (e.g. Genbank)
Author Response
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Round 2
Reviewer 1 Report
This revised manuscript presents a study on marine bacterial communities in the Xisha Islands, South China Sea. The authors have addressed all comments from a reviewer and improved the quality of the English. However, there are still a few issues that need to be resolved. After minor revisions, the manuscript may be considered for publication in Diversity.
1. According to the authors’ responses, the habitat of the benthic biological community consists mainly of coral and sandy coral bone bottoms. However, there is no data on the benthic biological community. The authors concluded that the distribution of bacterial communities in different regions is primarily influenced by pH, dissolved oxygen, and nutrients. Nutrients are strongly associated with the surrounding biological community, including macroalgae, fish, and coral. Some literature reports on the spatial distribution of benthic biological communities in the South China Sea may provide some clues. For example, an article was published in Diversity and Distributions (2021; 27: 929–943).
2. There are a few minor errors, such as “geuns” should be “genus” (line 295), “bacterialplankton” should be “bacterioplankton” (lines 20, 233, 284), and “fluctu-ation” should be “fluctuation” (line 373).
Author Response
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Reviewer 2 Report
# You should not use past tense in your introduction or abstract i.e. Prokaryotes represented the majority of diversity on the planet. You do this a lot in your manuscript and it is not nice.
# the whole $4.3 regarding FAPROTAX needs revising. Of course a bacterium can perform multiple functions!!!! This is not something new!!! What about SAR11 and other groups as well? Did you find these functions in your samples from FAPROTAX or are your claims based on literature? This is not clearly mentioned anywhere in the text. You have to clarify
# also regarding Fig.9 , what do you mean with cumulative absolute abundances? What is the scale you use? Are these data log transformed. You should write all these things in your legend.
# also in $ 3.6 where are the significant differences. How were they calculated?
# I think you should have a closing paragraph with you conclusions. You cannot finish with assumptions derived from FAPROTAX
Author Response
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Round 3
Reviewer 2 Report
The authors have substantially improved the manuscript.
However I still disagree with data availabilty statement. The authors claim that 'The data that support the findings of this study have been uploaded to NCBI’s Genbank under accession number OQ804222-OQ804309.'
These are just 87 seven partial sequences that in no case match with the 75,421 OTUs the authors claim to have in their samples. Their data should be submitted to genbank as raw sequences in one or several bioprojects and not as random OTUs from their 88 samples.
Thus I have to reject this submission since I believe it is inappropriate to present as data supporting findings of a NGS project, random sequences with no further explanations
