Rodríguez-Barreras R et al. (2026), Seasonality shapes gut microbiota composition i...

ECB-ART-54812

PeerJ 2026 Mar 05;14:e20918. doi: 10.7717/peerj.20918.

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Seasonality shapes gut microbiota composition in two sympatric sea urchins.

Rodríguez-Barreras R, Suárez-Pérez J, Godoy-Vitorino F.

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BACKGROUND: The gut microbiota plays critical roles in digestion, immunity, and environmental adaptation in marine invertebrates. Its composition is shaped by both host traits and abiotic factors such as temperature and seasonality. In Caribbean reefs, sea urchins like Diadema antillarum and Echinometra lucunter are important grazers that regulate algal biomass and influence benthic community dynamics. This study used 16S rRNA gene sequencing to compare, for the first time, the gut microbiota of these two sympatric species across contrasting seasons. METHODS: Adults of D. antillarum and E. lucunter were collected during summer and winter from three fringing reefs in Puerto Rico. Gut contents were extracted under sterile conditions, and bacterial DNA was extracted amplified for their 16S rRNA genes and sequenced. Microbial diversity and structure were assessed standard microbiota pipelines. RESULTS: Microbial communities in both echinoids were dominated by Bacillota, Bacteroidota, Desulfobacterota, and Pseudomonadota. Core microbiota analysis revealed stable taxa across hosts and seasons, most notably Propionigenium, supporting host-driven selection mechanisms that maintain functional stability despite seasonal turnover. Core microbiome analyses revealed Bacillota, Bacteroidota, Desulfobacterota_G_459543, and Pseudomonadota as persistent phyla across seasons, and genera such as Desulfotalea, Photobacterium, and Propionigenium consistently present in both species. Alpha diversity was significantly higher in winter for both D. antillarum and E. lucunter, while species-level differences were not significant. Beta diversity analyses showed significant seasonal clustering, with no consistent segregation between species within seasons. Our findings demonstrate that shared environmental conditions, particularly seasonality, are the primary modulators of gut microbiota in sympatric sea urchins, while host selection preserves a conserved core community. This dual influence of environment and host highlights the ecological plasticity and resilience of sea urchin microbiotas under fluctuating reef conditions.

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	Figure 1. Gut microbiota structure and composition of sea urchins Diadema antillarum and Echinometra lucunter) across species and seasons (summer and winter).(A) PCoA analysis of Bray Curtis dissimilarities. (B) Alpha diversity indices (Chao1, Faith’s PD, Shannon, and Pielou). Taxonomic composition at the phylum (C) and genus level (D).
	Figure 2. Important feature selection by Random Forest at the Phylum (A) and Genus (B) levels, showing species-seasonal variations of the bacterial taxa.The plots display the taxonomic features of importance and are ranked based on the mean decrease in classification accuracy when permuted. “High” and “Low” refer to a higher and lower value respectively, of the importance of that taxon in predicting the group.
	Figure 3. Seasonal variation in the gut microbiota of the sea urchin Echinometra lucunter across seasons.(A) Principal Coordinates Analysis (PCoA) based on Bray-Curtis dissimilarities show a clear separation between summer and winter samples. (B) Alpha diversity metrics (Chao1, Faith’s PD, Shannon, and Pielou) comparing summer and winter gut microbiota. Random Forest importance plots for phylum-level (C) and genus-level (D) taxa.
	Figure 4. Genus-level core microbiome of the sea urchin Echinometra lucunter across prevalence thresholds.Number of core features at the genus level, limited to the ten most abundant genera, across prevalence thresholds (0.5–0.7). Core features were defined as taxa present in at least the specified fraction of samples.
	Figure 5. Seasonal variation in the gut microbiota of the sea urchin Diadema antillarum across seasons.(A) Principal Coordinates Analysis (PCoA) based on Bray-Curtis dissimilarities show a clear separation between summer and winter samples. (B) Alpha diversity metrics (Chao1, Faith’s PD, Shannon, Pielou). Random Forest importance plots for phylum-level (C) and genus-level (D) taxa.
	Figure 6. Genus-level core microbiome of the sea urchin Diadema antillarum across prevalence thresholds.Number of core features identified at the genus level across increasing prevalence thresholds (0.5–0.7). Only genera meeting the specified fraction of sample presence were retained as core members.