Microbial Communities’ Composition of Supralittoral and Intertidal Sediments in Two East African Beaches (Djibouti Republic)

Round 1

Reviewer 1 Report

Comments and Suggestions for Authors

Renzi et al. reported a case study of microbial communities on tropical sandy beaches. I believe the experimental design is well-executed, and the results are presented clearly, making the paper suitable for publication in Microbial Research. I offer a few minor suggestions for the authors to consider:

1. Methodology: The sequencing method should be referred to as amplicon sequencing rather than metagenomic sequencing. Based on the authors' description, the sequencing was limited to 16S rRNA rather than whole microbial genomes. Additionally, the PCR experimental conditions were not provided.

2. Limitations: The experimental results presented by the authors have limitations, which should be explicitly addressed in the discussion. First, in terms of sampling design, only one region was sampled, and no seasonal sampling was conducted, making it uncertain whether the results can be generalized. Furthermore, the authors speculate that the differences between rural and urban areas are related to human activity, which is too broad; a more specific explanation is needed. The influence of the intertidal gradient on microbial communities can be quantified with data, such as examining whether salinity correlates with the abundance of certain microbial taxa and calculating their correlation. A similar concern applies to the impact of sediment composition on microbial communities. If these improvements cannot be implemented, the limitations of the study should be explicitly stated in the conclusion.

Author Response

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Author Response File: Author Response.pdf

Reviewer 2 Report

Comments and Suggestions for Authors

This manuscript presents a comparative study of spatial variation in microbial communities (bacteria and fungi) in tropical coastal beach sediments. Based on 16S rRNA and ITS2 amplicon high-throughput sequencing, the study integrates granulometry and elemental composition analyses to explore the influence of anthropogenic activity and natural gradients (e.g., tidal zones) on microbial diversity and community structure.

 

Strengths:

Novelty of the topic: This is the first report on microbial communities from the eastern African coast, filling a regional research gap.

 

Rich dataset: The study includes granulometric data, elemental composition, alpha/beta diversity, differential abundance, and visualization, with detailed methodology.

 

Standardized methodology: Techniques such as Illumina MiSeq sequencing, DADA2, PERMANOVA, and ANCOM-BC are all commonly accepted and robust. The manuscript is generally well-written and logically structured.

 

Weaknesses:

English language quality needs polishing: While most sections are grammatically correct, there are lengthy, passive, or structurally convoluted sentences that hinder readability.

 

Insufficient depth in results and discussion: Some analytical conclusions lack causal reasoning or ecological interpretation.

 

Limited novelty: The study is mainly a baseline regional survey, with little exploration of functional genes, metabolic potential, or underlying ecological mechanisms. Some results are repetitive or could be consolidated, making the structure somewhat redundant.

 

Representativeness of the two beaches: While the study demonstrates differences between the two beach types, it remains unclear whether the observed differences are due to site-specific factors. Would including more sampling sites representing various beach types improve generalizability?

 

Detailed Review Comments:

1. Language and Grammar

The manuscript relies too heavily on passive voice, such as “was observed,” “was found,” and “were collected,” which affects the overall tone.

 

Some sentences are overly long and complex. For example:

 

"These peculiar environments are characterized by highly variable biotic and abiotic factors that produce unique dynamic physical properties, such as moisture levels and nutrient availability."

This could be split into two sentences to improve clarity.

 

1. Structure and Logic

Introduction is comprehensive but somewhat verbose. Background information on temperate/tropical research could be condensed to better emphasize the study’s significance.

 

Methods are very detailed. Consider trimming some parts to avoid redundancy, e.g., listing of reagent brands and instrument settings can be moved to Supplementary Materials.

 

Results are well-illustrated, but Figures 4 and 5 contain overlapping descriptions. Consolidating some findings and integrating differential abundance data into the Discussion would improve flow.

 

III. Experimental Design and Data Processing

Strengths:

 

Dual-marker sequencing (16S and ITS2) with >1 million reads, and a well-structured analysis pipeline (Cutadapt, DADA2, PERMANOVA, ANCOM-BC).

 

Comprehensive approach including alpha/beta diversity, differential abundance, and clustering analyses.

 

Areas for Improvement:

 

Replication details are unclear—are the 11 samples per site biological or technical replicates? If each transect point is a unique sample, the statistical power may be limited.

 

ANCOM-BC results lack details on FDR values or effect sizes (logFC)—these should be provided, at least in the Supplementary.

 

Functional predictions (e.g., using PICRUSt2 or FUNGuild) are absent. Even with amplicon data, inferred functional trends would enhance ecological interpretation.

 

Fungal results are comparatively weak, with limited spatial differentiation. The authors should consider whether this is due to ITS database limitations or sequencing depth.

 

1. Figures and Visualization

Figures 4 and 5 are informative but could benefit from enhanced color contrast, larger font sizes, and improved legibility of legends.

 

Figure 3 (elemental composition) might be better presented as boxplots or scatter plots instead of line graphs to more clearly show distributional differences.

 

Author Response

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Author Response File: Author Response.pdf

Reviewer 3 Report

Comments and Suggestions for Authors

The manuscript ‘Microbial communities’ composition of supralittoral and intertidal sediments in two East African beaches (Djibouti Republic)’ is devoted to the study of microbial communities in the tropical sandy beaches. The authors studied bacterial and fungal composition of two types beaches along 10-meter transects. In parallel, the authors studied the granulometric and elemental composition of the sandy beaches. The article is interesting and useful for this region, because such studies have not been conducted here. Its results can be used to compare microbial communities with other sandy beaches. The manuscript can be published after minor editing.

I have some minor comments.

1. Sequences should be registered in the NCBI database (SRA archive) and registration numbers should be given in the article.
2. It is better to add an inset to the map where these beaches are located. It is unclear how far these beaches are from each other.
3. It is unclear from what depth the sediment was taken. Or is it a surface sediment sample?
4. The coordinates of the second sampling point are missing.
5. Granulometric composition of sediment samples and comparison of elemental concentrations are given for all points (22 points) in figures 2-3. Data for six points are shown on the figures 4-5, because the authors combined the samples. So, authors should to combine the data for granulometric composition and elemental concentrations. Or still no combine the data in Figures 4-5.
6. Line 10 - It's not English.
7. Sometimes the authors italicize the genus, sometimes not (line 25-26).
8. The authors do not describe microbial diversity at the phylum level at all. It is difficult to understand how diverse the microbial community. In addition, it is unclear to which phylum discussed bacteria belong.

Author Response

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Author Response File: Author Response.pdf

Round 2

Reviewer 2 Report

Comments and Suggestions for Authors

The authors have thoroughly addressed the comments raised in the previous round of review. The revisions are comprehensive and significantly improve the clarity, scientific rigor, and overall quality of the manuscript. I appreciate the authors’ efforts in revising the manuscript and believe it is now suitable for publication in its current form.