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. 2020 Feb 3;8(1):8.
doi: 10.1186/s40168-019-0776-5.

Coral microbiome composition along the northern Red Sea suggests high plasticity of bacterial and specificity of endosymbiotic dinoflagellate communities

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Coral microbiome composition along the northern Red Sea suggests high plasticity of bacterial and specificity of endosymbiotic dinoflagellate communities

Eslam O Osman et al. Microbiome. .

Erratum in

Abstract

Background: The capacity of reef-building corals to tolerate (or adapt to) heat stress is a key factor determining their resilience to future climate change. Changes in coral microbiome composition (particularly for microalgal endosymbionts and bacteria) is a potential mechanism that may assist corals to thrive in warm waters. The northern Red Sea experiences extreme temperatures anomalies, yet corals in this area rarely bleach suggesting possible refugia to climate change. However, the coral microbiome composition, and how it relates to the capacity to thrive in warm waters in this region, is entirely unknown.

Results: We investigated microbiomes for six coral species (Porites nodifera, Favia favus, Pocillopora damicornis, Seriatopora hystrix, Xenia umbellata, and Sarcophyton trocheliophorum) from five sites in the northern Red Sea spanning 4° of latitude and summer mean temperature ranges from 26.6 °C to 29.3 °C. A total of 19 distinct dinoflagellate endosymbionts were identified as belonging to three genera in the family Symbiodiniaceae (Symbiodinium, Cladocopium, and Durusdinium). Of these, 86% belonged to the genus Cladocopium, with notably five novel types (19%). The endosymbiont community showed a high degree of host-specificity despite the latitudinal gradient. In contrast, the diversity and composition of bacterial communities of the surface mucus layer (SML)-a compartment particularly sensitive to environmental change-varied significantly between sites, however for any given coral was species-specific.

Conclusion: The conserved endosymbiotic community suggests high physiological plasticity to support holobiont productivity across the different latitudinal regimes. Further, the presence of five novel algal endosymbionts suggests selection of certain genotypes (or genetic adaptation) within the semi-isolated Red Sea. In contrast, the dynamic composition of bacteria associated with the SML across sites may contribute to holobiont function and broaden the ecological niche. In doing so, SML bacterial communities may aid holobiont local acclimatization (or adaptation) by readily responding to changes in the host environment. Our study provides novel insight about the selective and endemic nature of coral microbiomes along the northern Red Sea refugia.

Keywords: 16S rRNA gene profiling; Climate change; Coral acclimatization; Future Oceans; Holobiont; Microbial community; Symbiodiniaceae.

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Conflict of interest statement

The authors declare that they have no competing interests.

Figures

Fig. 1
Fig. 1
Endosymbiont distribution for six coral species collected from two depths (2–5 m and 15–18 m) along five different sites at the northern Red Sea (total n = 163). The map shows the long-term mean of sea surface temperature along the Red Sea and the thermal gradient in the northern Red Sea, including sampling sites. Data obtained from Giovanni Ocean color (https://giovanni.gsfc.nasa.gov/giovanni/, MODIS Aqua 4 km satellite, 4 μm night only) for the period between July 2002 and August 2018. The tile plot represents endosymbiont ITS2 types associated with each coral host, depth, and site separately where site represents a latitudinal gradient (sites on y-axis are arranged from the North (top) to South (bottom)). Three distinct patterns are apparent: (i) high degree of host-symbiont specificity, (ii) absence of depth-specific patterns, except for P. damicornis and F. favus, which changed the ratio of dominant clades with depth, and (iii) symbiont community within each host did not change across the latitudinal gradient, except in S.hystrix. White tiles represent missing samples; representative image of coral hosts above tile plot column for each respective species
Fig. 2
Fig. 2
Taxonomic profile (genus level) of the abundant bacterial community associated with the surface mucus layer of six coral species and surrounding seawater samples (left) collected from five surveyed sites (right) in the northern Red Sea. Alteromonas and Pseudoalteromonas were the most dominant OTUs and composed combined 43.6% of the total community in both sites and coral species, bacterial community was significantly different between sites and coral hosts. Water samples had markedly distinct bacterial assemblage: over 60% of the bacteria had less than 1% of relative abundance. Unclassified taxa to genus level were denoted by (UC)
Fig. 3
Fig. 3
Principal coordinate analysis (PCoA) based on Bray-Curtis dissimilarity matrix of bacterial communities associated with six coral species and five sites along the latitudinal gradient in the northern Red Sea. PCoA shows clustering pattern between coral species versus seawater (a) and between different sites (b). Two most abundant OTUs (Alteromonas sp. and Pseudoalteromonas sp.) mask geographic patterns and were therefore excluded for this visualization. Compositional differences in bacterial communities were best explained by site
Fig. 4
Fig. 4
Venn diagram illustrating the number of bacterial OTUs that are present in at least 95% of the samples at each site and coral species. The graph shows the number of core OTUs shared among coral species (a). Only five OTUs were common between six corals species and seawater, but seawater samples had 72 exclusive OTUs that were not found in the SML. Similarly, eight OTUs (49.7% of total bacterial abundance) were common between sites (b), five of them were shared between all species in addition to a Vibrio sp., a Gplla sp., and the photosynthetic Erythrobacter sp. Importantly, each site and coral species had a small number of exclusive OTUs (outer region in diagram)

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