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Sci Rep
2018 Oct 02;81:14636. doi: 10.1038/s41598-018-33007-8.
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Local confinement of disease-related microbiome facilitates recovery of gorgonian sea fans from necrotic-patch disease.
Quintanilla E
,
Ramírez-Portilla C
,
Adu-Oppong B
,
Walljasper G
,
Glaeser SP
,
Wilke T
,
Muñoz AR
,
Sánchez JA
.
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Microbiome disruptions triggering disease outbreaks are increasingly threatening corals worldwide. In the Tropical Eastern Pacific, a necrotic-patch disease affecting gorgonian corals (sea fans, Pacifigorgia spp.) has been observed in recent years. However, the composition of the microbiome and its disease-related disruptions remain unknown in these gorgonian corals. Therefore, we analysed 16S rRNA gene amplicons from tissues of healthy colonies (n = 19) and from symptomatic-asymptomatic tissues of diseased colonies (n = 19) of Pacifigorgia cairnsi (Gorgoniidae: Octocorallia) in order to test for disease-related changes in the bacterial microbiome. We found that potential endosymbionts (mostly Endozoicomonas spp.) dominate the core microbiome in healthy colonies. Moreover, healthy tissues differed in community composition and functional profile from those of the symptomatic tissues but did not show differences to asymptomatic tissues of the diseased colonies. A more diverse set of bacteria was observed in symptomatic tissues, together with the decline in abundance of the potential endosymbionts from the healthy core microbiome. Furthermore, according to a comparative taxonomy-based functional profiling, these symptomatic tissues were characterized by the increase in heterotrophic, ammonia oxidizer and dehalogenating bacteria and by the depletion of nitrite and sulphate reducers. Overall, our results suggest that the bacterial microbiome associated with the disease behaves opportunistically and is likely in a state of microbial dysbiosis. We also conclude that the confinement of the disease-related consortium to symptomatic tissues may facilitate colony recovery.
Figure 1. Sampling design of healthy and diseased colonies of Pacifigorgia cairnsi. (a) Healthy colony and (b) diseased colony affected by NPD at Malpelo Island. (c) Detail of P. cairnsi lesion showing tissue with extended polyps (1), tissue with retracted polyps (2) and necrotic areas lacking polyps and coenenchyme (3). (d) Diagram showing sampling design. Samples (5 × 5 cm) were taken from peripheral tissue of healthy colonies (HP), basal tissue of healthy colonies (HB), peripheral (symptomatic) tissue of diseased colonies (DP) and basal (but asymptomatic) tissue of diseased colonies (DB). Necrotic patches (NP) were not included in DP samples.
Figure 2. PCoA plots based on a Bray-Curtis dissimilarity matrix of bacterial community compositions in healthy and diseased P. cairnsi samples. (a) Community compositions from samples of healthy colonies (HB and HP) and (b) from samples of healthy and diseased colonies (HB, HP, DB and DP) were compared using Bray-Curtis dissimilarity metric on the square-root transformed relative abundances. Note that disease basal (DB) samples showed no symptoms of disease. Principal Coordinate Analysis was used for visualization purposes, and the first two components (explaining over 50% of the variation) are displayed. The number of samples from each type of tissue is indicated within parenthesis. Vectors’ numbers correspond to taxa assigned at OTUs level: (1) genus Mycoplasma, (2) genus Endozoicomonas, (3) genus Endozoicomonas, (4) order Bacteroidales, (5) genus Aquimarina, (6) family Oceanospirillaceae, (7) order Alteromonadales, (8) domain Bacteria, (9) order Kiloniellales, (10) class Alphaproteobacteria, (11) class Alphaproteobacteria, (12) genus Loktanella, (13) domain Bacteria, (14) family Pirellulaceae, (15) class Alphaproteobacteria, (16) order 34P16, (17) order Kiloniellales, (18) order Oceanospirillales, (19) family Rhodobacteraceae, (20) genus Polaribacter, (21) domain Bacteria, (22) genus Synechococcus, (23) class Spirochaetes, (24) order CAB-I, (42) genus Nitrosopumilus, (44) genus Vibrio, (45) species Polymorphum gilvum, (175) genus Endozoicomonas, (755) genus Endozoicomonas.
Figure 3. Heatmap of relative abundances of OTUs in tissue samples from healthy colonies. Eighteen OTUs that accounted for 95% of the cumulative abundance in healthy colonies are displayed, with the top seven OTUs corresponding to the core microbiome (g: genus, f: family, c: class, o: order). Samples (columns) were ordered according to their spatial position displayed along the first PCoA component (explaining over 30% of the variation, Fig. 2a).
Figure 4. Heatmap of the relative abundances of OTUs in tissue samples from healthy and diseased colonies. According to the SIMPER analyses, the eleven OTUs depicted mainly contributed to the differentiation between symptomatic (DP) and asymptomatic samples (HB, HP, DB), (g: genus, f: family, c: class, o: order). Average dissimilarity (%) corresponds to OTU’s contribution to the dissimilarity between DP and the rest of samples (DB, HP and HB).
Figure 5. Taxonomy-based functional profiling of bacterial communities in samples from healthy and diseased colonies. Shifts in potential functional differences are represented by a relative abundance scale showing the enrichment (red colour) and depletion (blue colour) in different metabolic profiles mapped to the corresponding taxonomic information by METAGENassist. Hierarchical clustering of samples and functions was performed by a single linkage algorithm using Euclidean distance measurements.
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