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Sci Rep
2020 Dec 08;101:21443. doi: 10.1038/s41598-020-78534-5.
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Composition and geographic variation of the bacterial microbiota associated with the coelomic fluid of the sea urchin Paracentrotus lividus.
Faddetta T
,
Ardizzone F
,
Faillaci F
,
Reina C
,
Palazzotto E
,
Strati F
,
De Filippo C
,
Spinelli G
,
Puglia AM
,
Gallo G
,
Cavalieri V
.
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In the present work, culture-based and culture-independent investigations were performed to determine the microbiota structure of the coelomic fluid of Mediterranean sea urchin Paracentrotus lividus individuals collected from two distinct geographical sites neighboring a high-density population bay and a nature reserve, respectively. Next Generation Sequencing analysis of 16S rRNA gene (rDNA) showed that members of the Proteobacteria, Bacteroidetes and Fusobacteria phyla, which have been previously reported to be commonly retrieved from marine invertebrates, dominate the overall population of microorganisms colonizing this liquid tissue, with minority bacterial genera exhibiting remarkable differences among individuals. Our results showed that there is a correlation between microbiota structure and geographical location of the echinoderm collection site, highlighting over-representation of metagenomic functions related to amino acid and bioactive peptides metabolism in specimens inhabiting the nature reserve. Finally, we also described the developmental delay and aberrations exhibited by sea urchin embryos exposed to distinct bacterial isolates, and showed that these defects rely upon hydrophilic compound(s) synthesized by the bacterial strains assayed. Altogether, our findings lay the groundwork to decipher the relationships of bacteria with sea urchins in their aquatic environment, also providing an additional layer of information to understand the biological roles of the coelomic fluid.
Figure 1. Mean relative abundances of taxa, at genus level, of the coelomic fluid microbiota of P. lividus individuals collected from sites A and B. The corresponding phylum is highlighted by using shades of blue, green, and orange for Proteobacteria, Fusobacteria and Bacteroidetes, respectively. All bacterial genera with relative abundanceâ<â1% are reported together and labeled as âOthersâ. The underlined taxa represent the microbiota core members.
Figure 2. Comparative analysis of the most discriminant bacterial taxa in the coelomic microbiota of P. lividus individuals from site A vs site B. Log10 of LDA scores was calculated for the most discriminant bacterial taxa identified by LEfSe. Positive and negative LDA scores indicate the taxa enriched in the coelomic microbiota of P. lividus specimens from A and site B sites, respectively. Only taxa having a pâ<â0.05 (Wilcoxon rank-sum test) and LDAâ>|2.0| are shown.
Figure 3. Putative functional capabilities differentially represented in the coelomic microbiota of specimens from A and B sites. A total of 7 differentially represented (pâ<â0.01) metabolic pathways were inferred by Piphillin using the KEGG database80.
Figure 4. Optimal phylogenetic tree of the six cultivable bacterial strains isolated from coelomic fluid of P. lividus specimens collected in A (A1â4) and B (B1â2) sites. The analysis involved 48 nucleotide sequences. The evolutionary history and distances were obtained using neighbor-joining and the maximum composite likelihood methods, respectively. Distances are in the units of the number of base substitutions per site.
Figure 5. Developmental effects of coelomic fluid bacterial strain exposure on P. lividus. Representative embryos cultured in the absence (control) or in the presence of the indicated bacterial strains, bacterial lysate supernatants or equivalent amounts of methanolic extracts, and observed at the pluteus stage.
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