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Front Microbiol
2019 Jan 01;10:1168. doi: 10.3389/fmicb.2019.01168.
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The Composition, Diversity and Predictive Metabolic Profiles of Bacteria Associated With the Gut Digesta of Five Sea Urchins in Luhuitou Fringing Reef (Northern South China Sea).
Yao Q
,
Yu K
,
Liang J
,
Wang Y
,
Hu B
,
Huang X
,
Chen B
,
Qin Z
.
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Sea urchins strongly affect reef ecology, and the bacteria associated with their gut digesta have not been well studied in coral reefs. In the current study, we analyze the bacterial composition of five sea urchin species collected from Luhuitou fringing reef, namely Stomopneustes variolaris, Diadema setosum, Echinothrix calamaris, Diadema savignyi, and Tripneustes gratilla, using high-throughput 16S rRNA gene-based pyrosequencing. Propionigenium, Prolixibacter, and Photobacterium were found to be the dominant bacterial genera in all five species. Interestingly, four sea urchin species, including S. variolaris, D. setosum, E. calamaris, and D. savignyi, displayed a higher mean total abundance of the three bacterial genera (69.72 ± 6.49%) than T. gratilla (43.37 ± 13.47%). Diversity analysis indicated that the gut digesta of sea urchin T. gratilla displayed a higher bacterial α-diversity compared with the other four species. PCoA showed that the four groups representing D. setosum, D. savignyi, E. calamaris, and S. variolaris were overlapping, but distant from the group representing T. gratilla. Predictive metagenomics performed by PICRUSt revealed that the abundances of genes involved in amino acid metabolism and metabolism of terpenoid and polyketide were higher in T. gratilla, while those involved in carbohydrate metabolism were higher in the other four sea urchin species. Therefore, our results indicated that the composition, diversity and predictive metabolic profiles of bacteria associated with the gut digesta of T. gratilla were significantly different from those of the other four sea urchin species in Luhuitou fringing reef.
FIGURE 1. Map of study area. Sampling area represented by red circle and star.
FIGURE 2. The morphological forms of all five sea urchin species in our study; (A)
D. savignyi; (B)
D. setosum; (C)
E. calamaris; (D)
S. variolaris; (E)
T. gratilla.
FIGURE 3. The gut bacterial community profiles of individual sea urchins at the phylum level. The horizontal axis represents the percentage of each phylum. Each bar represents the community of an individual sea urchin. Others denote those phyla whose abundances were less than 0.01%. W1–5 denote the five replicates of E. calamaris; M2–5, M7–8, and M10 denote the seven replicates of D. setosum; K1–3 and K5 denote the four replicates of S. variolaris; G1–3 and G5 denote the four replicates D. savignyi; B1–18 and B20–21 denote the 20 replicates T. gratilla.
FIGURE 4. The gut bacterial community profiles of all individual sea urchins at the genus level. The horizontal axis represents the percentage of each genus. Each bar represents the community of an individual sea urchin. Others denote those genus whose abundances were less than 0.01%. Please refer to Figure 3 for sample identification.
FIGURE 5. PCoA of the gut bacterial community of sea urchins at the genus level based on the subsampled unweighted UniFrac distance matrix at the genus level. PC1 and PC2 explained 28.95 and 11.22% of the total variance, respectively. For sample identification, please refer to Figure 3.
FIGURE 6. PICRUSt (V1.0.0) analysis of predicted metagenomes using the 16S rRNA gene data of gut digesta bacteria of D. savignyi, D. setosum, E. calamaris, S. variolaris, and T. gratilla. (A) The mean relative abundance of all metabolic pathways in KEGG level 2 in the five sea urchin species. The error bars denote the standard deviation. (B) Box plots of the KEGG level 2 categories of carbohydrate metabolism, amino acid metabolism and metabolism of terpenoids and polyketides analyzed by STAMP v2.1.0 software. The p-values of each KEGG level 2 analysis are displayed in the box plot.
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