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Trophic niches reflect compositional differences in microbiota among Caribbean sea urchins.
Rodríguez-Barreras R
,
Tosado-Rodríguez EL
,
Godoy-Vitorino F
.
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Sea urchins play a critical role in marine ecosystems, as they actively participate in maintaining the balance between coral and algae. We performed the first in-depth survey of the microbiota associated with four free-living populations of Caribbean sea urchins: Lytechinus variegatus, Echinometra lucunter, Tripneustes ventricosus, and Diadema antillarum. We compared the influence of the collection site, echinoid species and trophic niche to the composition of the microbiota. This dataset provides a comprehensive overview to date, of the bacterial communities and their ecological relevance associated with sea urchins in their natural environments. A total of sixty-samples, including surrounding reef water and seagrass leaves underwent 16S rRNA gene sequencing (V4 region) and high-quality reads were analyzed with standard bioinformatic approaches. While water and seagrass were dominated by Cyanobacteria such as Prochlorococcus and Rivularia respectively, echinoid gut samples had dominant Bacteroidetes, Proteobacteria and Fusobacteria. Propionigenium was dominant across all species' guts, revealing a host-associated composition likely responsive to the digestive process of the animals. Beta-diversity analyses showed significant differences in community composition among the three collection sites, animal species, and trophic niches. Alpha diversity was significantly higher among L. variegatus samples compared to the other species. L. variegatus also displayed an increased abundance of Planctomycetes and Cyanobacterial OTUs. The bacterial community of this herbivorous echinoid reflected similarities to the microfilm community found on Thalassia testudinum leaves; a very abundant seagrass and its main food resource. The results of this study elaborate on the microbial ecology of four important Caribbean echinoids, confirming that selection on the microbial community is trophic-niche dependent.
Figure 1. Overview of sample sites in the Northeastern coast of Puerto Rico.Cerro Gordo in Vega Baja (CG), Isla de Cabra in Cataño (IC), and Mar Azul in Luquillo (MA).
Figure 2. Diversity analyses comparing sample types, including water, seagrass and gut samples from the four sea urchin species.Bray-Curtis analysis represented by a 2D Principal Coordinates Analysis (PCoA) using sample types as metadata categories (A). PERMANOVA showed significant differences in beta diversity (PERMANOVA p-value = 0.01, ANOSIM p-value =0.001). T-tests on the alpha diversity curves demonstrated that seawater and seagrass environments were significantly more diverse than gut samples (p-value = 0.003). Bar Plots depict relative abundance of bacteria at the phyla (C), and genus levels (D).
Figure 3. Diversity analyses comparing the four sea urchin species.Bray-Curtis analysis represented in a 2D Principal Coordinates Analysis (PCoA) using species as metadata categories, depicts distinct species clustering with PERMANOVA p-value =0.004; ANOSIM p-value =0.01 (A). Rarefaction curves of Chao1 index demonstrated significant differences between green (Lytechinus_variegatus) and red (Echinometra_lucunter) sea urchin (p-value =0.006) and between red (Echinometra_lucunter) and black (Diadema_antillarum) sea urchin (p-value =0.048) (B). Species relative abundance at phyla (C) and genus levels (D) are depicted by the bar plots.
Figure 4. Diversity analyses comparing the three sampling sites: Cerro Gordo, Cataño and Luquillo.Bray-Curtis analysis, represented by an NMDS (stress 0.121003), used collection sites and sea urchin species as metadata categories. PERMANOVA showed significant differences in beta diversity (p-value = 0.001, ANOSIM p-value = 0.01) (A). Alpha diversity as shown by the rarefaction curves did not demonstrate any significant differences between sites (B). Bar Plots depict relative abundance at phyla level (C). When combining species and site, richness was not significantly different although the green sea urchin (Lytechinus_variegatus) seems more diverse (D). Bacterial genus-level plots among species distributed by site are depicted in (E). LEFSE shows genus level taxa that are more dominant per each species distributed by collection site (F).
Figure 5. Boxplots of bacterial genus-level analyses (assigned per phylum) that discriminate among the four sea urchin species (p-values < 0.05 marked with an asterisk).
Figure 6. Diversity analyses comparing sea urchin trophic niches (animals collected in the reef or among seagrass).Bray-Curtis analysis is represented by a 2D Principal Coordinates Analysis (PCoA) PERMANOVA p-value = 0.007; ANOSIM p-value = 0.01 (A). Chao 1 alpha diversity rarefaction curves show no significant differences between trophic niches (p-value = 0.704) (B). Bar Plots depict relative abundance at phyla (C), and genus-levels (D).
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