Biodiversity of Nematodes from Coral Reef Sediments in the South China Sea Based on eDNA Metabarcoding

Round 1

Reviewer 1 Report

Comments and Suggestions for Authors

It is an article with interesting data, with a novel methodology for a group of organisms that are difficult to study and with a very important ecological function. However, the article cannot be published in its current form due to several problems:

The introduction is non-existent. First, it has no citations, even though figures and percentages are given. Then, there is no account of previous studies on the topic, nor how this study contributes to filling a gap in knowledge. I was worried that this moment would come in writing scientific papers but it came. I ask the authors: How did they make the introduction? The writing style is very different from the rest of the article.

- The first two sentences of the results must go in methods.

- The third sentence of the results has two extra commas before 1,659,263

- In the eighth sentence we talk about “254 endemic OTUs”. The term endemic is misused, perhaps they meant “exclusive”.-       “At the level of order, Enoplea and Chromadorea are the dominant groups; at the level of phylum, mainly include Mermithida, Rhabditida, Plectida, Enoplida, and Dorylaimida;” Change to “At the level of class….” Then “at the level of order”.

-       Fig 2. Is it really necessary?

-       Table 2. High relative abundance…  How high? What do you mean.

-       In the discussion: “high in coral reef sediments in the South China Sea”, high compared to what?

-       Mention that Enoplea and Chromadorea are classes to avoid confusion.

-       “In contrast to the present study” What do you mean? If you are reffering to the Maldives study you have to say “to the mentioned study” or similar.

-       Overall, you do a lot of comparison with a study confused on meiofaina. Your study covers more that meiofauna since you are using a whole sediment sample, please state that clearly.

Author Response

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Author Response File: Author Response.docx

Reviewer 2 Report

Comments and Suggestions for Authors

Comment 1 (Materials, 2.1 Sample collection): The samples for this study were collected in April-May 2023 in the coral reef waters of the Nansha Islands(three stations on Beiwai shoal(BW1, BW2 and BW3); two stations on Meiji Reef(MJ2 and MJ4); one station on Chigua Reef(CG1); one station on Dongmen Reef(DM1); and one station on Zhangxi Reef(ZX1)), the Zhongsha Islands(one station on Walker Shoal:(MB)) and the Xisha Islands(three stations on North Reef(BJ1, BJ3 and BJ4); one station on Ganquan Reef(GQ); two stations on Qilian island(QLY1, QLY2)), with a total of 16 sampling stations.

This only 15 sampling stations, where got 16 sampling stations?

Comment 2 (Methods, 2.2 High-throughput sequencing): 3 replicates were set up for all the samples, and the PCR products of the same samples were mixed and checked by electrophoresis on 2% agarose gel. Qualified PCR products were subjected to library preparation and high-throughput sequencing on the Illumina MiSeq PE250 sequencing platform.

Why the authors need to have 3 replicates for all the samples? And the PCR products of the same samples were mixed and checked?

Comment 3 (Results): I cannot find the Table 1?

Comment 4 (Results 3.1): Table 2 shows the shared OTUs with high abundance in the two waters. At the level of order, Enoplea and Chromadorea are the dominant groups; at the level of phylum, mainly include Mermithida, Rhabditida, Plectida, Enoplida, and Dorylaimida;

I cannot understand what the high abundance been mentioned in the two waters.

Comment 5 (Results 3.3): at the genus level, mainly include Acrobeles (24.56%), Aporcelaimellus (13.61%), Hexamermis (12.74%), Criconemoides (9.93%), and Alaimus(8.33%); at the genus level, Acrobeles sp. MA-2012 ( 24.56%), Aporcelaimellus sp. JH-2004 (13.61%), Hexamermis albicans (12.74%), Criconemoides myungsugae (9.93%) and Alaimus sp. 1247 (8.32%) take the major part.

Something wrong in this? Why the authors need to descript twice the genus level?

Comment 6 (Figure 4): This figure is difficult to read, we cannot be distinguished by obvious colour easily within the Class, Order , Family...

Comment 7 (Result 3.5): Redundancy Analysis (RDA) was chosen for the analysis
of the relationship between the environmental factors and nematode community structure, and the environmental factors were chosen to be the conventional indexes (Latitude (LAT), total nitrogen (TN), total phosphorus (TP)) and heavy metal indicators (copper (Cu), zinc (Zn), cadmium (Cd), lead (Pb), arsenic (As)), and nematodes will be the genus as the analytical ordinal.

The authors did not mention how to the environment factors (conventional indexes (Latitude (LAT), total nitrogen (TN), total phosphorus (TP)) and heavy metal indicators (copper(Cu), zinc (Zn), cadmium (Cd), lead (Pb), arsenic (As)) been collected for analyse?

Comment 8 (Pg. 4): The authors may cite a not related paper “using LEfSE[8] to identify communities or species that significantly differed in their impact on sample partitioning.”

The LEfSE [8] are talking about “Microbial indicators of environmental perturbations in coral reef ecosystems. Microbiome 2019, 7, doi:10.1186/s40168-019-0705-7”

Please recheck and cite the more related references.

Comment 9 (Discussion): The authors should share the raw data (Appendix Table) of the 474 OTUs in 16 sediment samples been detected.

Author Response

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Author Response File: Author Response.docx

Round 2

Reviewer 1 Report

Comments and Suggestions for Authors

The authors improve his manuscript and followed all the recomendations. 

Comments on the Quality of English Language

They can double check the writing style in their results and discusion. 

Author Response

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Author Response File: Author Response.docx

Reviewer 2 Report

Comments and Suggestions for Authors

I can't find any correction in the revision manuscript for the Comment 5 (Results3.3)?

The Table 2 has been revised to "Species annotations of shared OTUs with high abundance in two regions of the South China Sea. BUT, the data shows in the Table 2 not identified to species level? 

Author Response

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Author Response File: Author Response.docx